From 57dc7d32d410f820027b160cb134595feb6ae364 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 23 Dec 2015 17:07:47 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14399 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 34 ++++++++++----------- doc/Section_commands.txt | 1 + doc/fix_nh.html | 24 +++++++++++---- doc/fix_qeq.html | 58 +++++++++++++++++++++++------------ doc/fix_qeq.txt | 64 ++++++++++++++++++++++++++------------- doc/searchindex.js | 2 +- 6 files changed, 119 insertions(+), 64 deletions(-) diff --git a/doc/Section_commands.html b/doc/Section_commands.html index df5bf412b3..37d41dab88 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -607,12 +607,12 @@ This is indicated by additional letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

--+++--+ @@ -692,59 +692,59 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

+ - - + + - - + + - - + + - - + + - - + + - - - + + diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 4a8446fbf2..f259ff6d7d 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -548,6 +548,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "property/atom"_fix_property_atom.html, "qeq/comb (o)"_fix_qeq_comb.html, "qeq/dynamic"_fix_qeq.html, +"qeq/fire"_fix_qeq.html, "qeq/point"_fix_qeq.html, "qeq/shielded"_fix_qeq.html, "qeq/slater"_fix_qeq.html, diff --git a/doc/fix_nh.html b/doc/fix_nh.html index 1b3f276711..72a2edb7ae 100644 --- a/doc/fix_nh.html +++ b/doc/fix_nh.html @@ -235,12 +235,12 @@ correctly, the time-averaged temperature and stress tensor of the particles will match the target values specified by Tstart/Tstop and Pstart/Pstop.

The equations of motion used are those of Shinoda et al in -(Shinoda), which combine the hydrostatic equations of -Martyna, Tobias and Klein in (Martyna) with the strain +(Shinoda), which combine the hydrostatic equations of +Martyna, Tobias and Klein in (Martyna) with the strain energy proposed by Parrinello and Rahman in -(Parrinello). The time integration schemes closely +(Parrinello). The time integration schemes closely follow the time-reversible measure-preserving Verlet and rRESPA -integrators derived by Tuckerman et al in (Tuckerman).

+integrators derived by Tuckerman et al in (Tuckerman).

The thermostat parameters for fix styles nvt and npt is specified using the temp keyword. Other thermostat-related keywords are @@ -397,7 +397,7 @@ freedom. A value of 0 corresponds to no thermostatting of the barostat variables.

The mtk keyword controls whether or not the correction terms due to Martyna, Tuckerman, and Klein are included in the equations of motion -(Martyna). Specifying no reproduces the original +(Martyna). Specifying no reproduces the original Hoover barostat, whose volume probability distribution function differs from the true NPT and NPH ensembles by a factor of 1/V. Hence using yes is more correct, but in many cases the difference is @@ -406,7 +406,7 @@ negligible.

scheme at little extra cost. The initial and final updates of the thermostat variables are broken up into tloop substeps, each of length dt/tloop. This corresponds to using a first-order -Suzuki-Yoshida scheme (Tuckerman). The keyword ploop +Suzuki-Yoshida scheme (Tuckerman). The keyword ploop does the same thing for the barostat thermostat.

The keyword nreset controls how often the reference dimensions used to define the strain energy are reset. If this keyword is not used, @@ -548,6 +548,18 @@ the outermost rRESPA timestep, the barostat dynamics are not the limiting factor for numerical stability. Both factorizations are time-reversible and can be shown to preserve the phase space measure of the underlying non-Hamiltonian equations of motion.

+
+

Note

+

This implementation has been shown to conserve linear momentum +up to machine precision under NVT dynamics. Under NPT dynamics, +for a system with zero initial total linear momentum, the total +momentum fluctuates close to zero. It may occasionally undergo brief +excursions to non-negligible values, before returning close to zero. +Over long simulations, this has the effect of causing the center-of-mass +to undergo a slow random walk. This can be mitigated by resetting +the momentum at infrequent intervals using the +fix momentum command.

+

The fix npt and fix nph commands can be used with rigid bodies or mixtures of rigid bodies and non-rigid particles (e.g. solvent). But diff --git a/doc/fix_qeq.html b/doc/fix_qeq.html index ce1f09f5c3..b1ac3f20c7 100644 --- a/doc/fix_qeq.html +++ b/doc/fix_qeq.html @@ -135,42 +135,53 @@

fix qeq/dynamic command

+
+
+

fix qeq/fire command

Syntax

-
fix ID group-ID style Nevery cutoff tolerance maxiter qfile
+
fix ID group-ID style Nevery cutoff tolerance maxiter qfile keyword ...
 

 

 
    
 
  • ID, group-ID are documented in fix command
    • 
-
  • style = qeq/point or qeq/shielded or qeq/slater or qeq/dynamic
    • 
+
  • style = qeq/point or qeq/shielded or qeq/slater or qeq/dynamic or qeq/fire
    • 
 
  • Nevery = perform charge equilibration every this many steps
    • 
 
  • cutoff = global cutoff for charge-charge interactions (distance unit)
    • 
 
  • tolerance = precision to which charges will be equilibrated
    • 
 
  • maxiter = maximum iterations to perform charge equilibration
    • 
 
  • qfile = a filename with QEq parameters
    • 
+
  • zero or more keyword/value pairs may be appended
    • 
+
  • keyword = alpha or qdamp or qstep
    • 
 

+
+alpha value = Slater type orbital exponent (qeq/slater only)
+qdamp value = damping factor for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
+qstep value = time step size for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
+

Examples

fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
 fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
-fix 1 all qeq/slater 5 10 1.0e-6 100 params
+fix 1 all qeq/slater 5 10 1.0e-6 100 params alpha 0.2
 fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq
+fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1

Description

-

Perform the charge equilibration (QEq) method as described in (Rappe and Goddard) and formulated in (Nakano) (also known -as the matrix inversion method) and in (Rick and Stuart) (also +

Perform the charge equilibration (QEq) method as described in (Rappe and Goddard) and formulated in (Nakano) (also known +as the matrix inversion method) and in (Rick and Stuart) (also known as the extended Lagrangian method) based on the electronegativity equilization principle.

These fixes can be used with any pair style in LAMMPS, so long as per-atom charges are defined. The most typical use-case is in conjunction with a pair style that performs charge equilibration periodically (e.g. every timestep), such -as the ReaxFF or Streitz-Mintmire potential (the latter is not yet -implemented in LAMMPS). But these fixes can also be used with +as the ReaxFF or Streitz-Mintmire potential. +But these fixes can also be used with potentials that normally assume per-atom charges are fixed, e.g. a Buckingham or LJ/Coulombic potential.

Because the charge equilibration calculation is effectively @@ -214,8 +225,8 @@ below, thus the others can be set to 0.0 if desired.

  • chi = electronegativity in energy units
  • eta = self-Coulomb potential in energy units
  • gamma = shielded Coulomb constant defined by ReaxFF force field in distance units
    • -
  • zeta = Slater type orbital exponent defined by the Streitz-Mintmire potential in reverse distance units
    • -
  • qcore = charge of the nucleus defined by the Streitz-Mintmire potential potential in charge units
    • +
  • zeta = Slater type orbital exponent defined by the Streitz-Mintmire potential in reverse distance units
    • +
  • qcore = charge of the nucleus defined by the Streitz-Mintmire potential potential in charge units

    • The qeq/point style describes partial charges on atoms as point charges. Interaction between a pair of charged particles is 1/r, @@ -239,27 +250,35 @@ charge densities centered around atoms via the Slater 1*s* orbital, so that the interaction between a pair of charged particles is the product of two Slater 1*s* orbitals. The expression for the Slater 1*s* orbital is given under equation (6) of the -Streitz-Mintmire paper. Only the chi, eta, zeta, and +Streitz-Mintmire paper. Only the chi, eta, zeta, and qcore parameters from the qfile file are used. This style solves partial charges on atoms via the matrix inversion method. A tolerance -of 1.0e-6 is usually a good number.

    +of 1.0e-6 is usually a good number. Keyword alpha can be used to +change the Slater type orbital exponent.

    The qeq/dynamic style describes partial charges on atoms as point charges that interact through 1/r, but the extended Lagrangian method is used to solve partial charges on atoms. Only the chi and eta parameters from the qfile file are used. Note that Coulomb catastrophe can occur if repulsion between the pair of charged particles is too weak. A tolerance of 1.0e-3 is usually a good -number.

    +number. Keyword qdamp can be used to change the damping factor, while +keyword qstep can be used to change the time step size.

    +

    The *qeq/fire* style describes the same charge model and charge +solver as the qeq/dynamic style, but employs a FIRE minimization +algorithm to solve for equilibrium charges. +Keyword qdamp can be used to change the damping factor, while +keyword qstep can be used to change the time step size.

    Note that qeq/point, qeq/shielded, and qeq/slater describe different charge models, whereas the matrix inversion method and the -extended Lagrangian method (qeq/dynamic) are different solvers.

    -

    Note that the qeq/point and the qeq/dynamic styles both describe +extended Lagrangian method (qeq/dynamic and qeq/fire) are +different solvers.

    +

    Note that qeq/point, qeq/dynamic and qeq/fire styles all describe charges as point charges that interact through 1/r relationship, but -solve partial charges on atoms using different solvers. Styles -qeq/point and the qeq/dynamic should yield comparable results if +solve partial charges on atoms using different solvers. These three +styles should yield comparable results if the QEq parameters and Nevery, cutoff, and tolerance are the -same. Style qeq/point is typically faster, but qeq/dynamic scales -better on larger sizes.

    +same. Style qeq/point is typically faster, qeq/dynamic scales +better on larger sizes, and qeq/fire is faster than qeq/dynamic.

    Note

    To avoid the evaluation of the derivative of charge with respect @@ -269,7 +288,7 @@ zero net charge.

    Note

    Developing QEq parameters (chi, eta, gamma, zeta, and qcore) is -an “art”. Charges on atoms are not guaranteed to equilibrate with +non-trivial. Charges on atoms are not guaranteed to equilibrate with arbitrary choices of these parameters. We do not develop these QEq paramters. See the examples/qeq directory for some examples.

    @@ -301,6 +320,7 @@ Chemistry, 95, 3358-3363 (1991).

    16, 11996 (1994)

    (ReaxFF) A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J Physical Chemistry, 105, 9396-9049 (2001)

    +

    (QEq/Fire) T.-R. Shan, A. P. Thompson, S. J. Plimpton, in preparation

    diff --git a/doc/fix_qeq.txt b/doc/fix_qeq.txt index a413c80b1b..daa22f3312 100644 --- a/doc/fix_qeq.txt +++ b/doc/fix_qeq.txt @@ -10,25 +10,35 @@ fix qeq/point command :h3 fix qeq/shielded command :h3 fix qeq/slater command :h3 fix qeq/dynamic command :h3 +fix qeq/fire command :h3 [Syntax:] -fix ID group-ID style Nevery cutoff tolerance maxiter qfile :pre +fix ID group-ID style Nevery cutoff tolerance maxiter qfile keyword ... :pre -ID, group-ID are documented in "fix"_fix.html command -style = {qeq/point} or {qeq/shielded} or {qeq/slater} or {qeq/dynamic} -Nevery = perform charge equilibration every this many steps -cutoff = global cutoff for charge-charge interactions (distance unit) -tolerance = precision to which charges will be equilibrated -maxiter = maximum iterations to perform charge equilibration -qfile = a filename with QEq parameters :ul +ID, group-ID are documented in "fix"_fix.html command :ulb,l +style = {qeq/point} or {qeq/shielded} or {qeq/slater} or {qeq/dynamic} or {qeq/fire} :l +Nevery = perform charge equilibration every this many steps :l +cutoff = global cutoff for charge-charge interactions (distance unit) :l +tolerance = precision to which charges will be equilibrated :l +maxiter = maximum iterations to perform charge equilibration :l +qfile = a filename with QEq parameters :l + +zero or more keyword/value pairs may be appended :l +keyword = {alpha} or {qdamp} or {qstep} :l + {alpha} value = Slater type orbital exponent (qeq/slater only) + {qdamp} value = damping factor for damped dynamics charge solver (qeq/dynamic and qeq/fire only) + {qstep} value = time step size for damped dynamics charge solver (qeq/dynamic and qeq/fire only) :pre + +:ule [Examples:] fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1 fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2 -fix 1 all qeq/slater 5 10 1.0e-6 100 params -fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq :pre +fix 1 all qeq/slater 5 10 1.0e-6 100 params alpha 0.2 +fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq +fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1 :pre [Description:] @@ -42,8 +52,8 @@ These fixes can be used with any "pair style"_pair_style.html in LAMMPS, so long as per-atom charges are defined. The most typical use-case is in conjunction with a "pair style"_pair_style.html that performs charge equilibration periodically (e.g. every timestep), such -as the ReaxFF or Streitz-Mintmire potential (the latter is not yet -implemented in LAMMPS). But these fixes can also be used with +as the ReaxFF or Streitz-Mintmire potential. +But these fixes can also be used with potentials that normally assume per-atom charges are fixed, e.g. a "Buckingham"_pair_buck.html or "LJ/Coulombic"_pair_lj.html potential. @@ -119,7 +129,8 @@ product of two Slater 1{s} orbitals. The expression for the Slater "Streitz-Mintmire"_#Streitz paper. Only the {chi}, {eta}, {zeta}, and {qcore} parameters from the {qfile} file are used. This style solves partial charges on atoms via the matrix inversion method. A tolerance -of 1.0e-6 is usually a good number. +of 1.0e-6 is usually a good number. Keyword {alpha} can be used to +change the Slater type orbital exponent. The {qeq/dynamic} style describes partial charges on atoms as point charges that interact through 1/r, but the extended Lagrangian method @@ -127,26 +138,34 @@ is used to solve partial charges on atoms. Only the {chi} and {eta} parameters from the {qfile} file are used. Note that Coulomb catastrophe can occur if repulsion between the pair of charged particles is too weak. A tolerance of 1.0e-3 is usually a good -number. +number. Keyword {qdamp} can be used to change the damping factor, while +keyword {qstep} can be used to change the time step size. + +The "{qeq/fire}"_#Shan style describes the same charge model and charge +solver as the {qeq/dynamic} style, but employs a FIRE minimization +algorithm to solve for equilibrium charges. +Keyword {qdamp} can be used to change the damping factor, while +keyword {qstep} can be used to change the time step size. Note that {qeq/point}, {qeq/shielded}, and {qeq/slater} describe different charge models, whereas the matrix inversion method and the -extended Lagrangian method ({qeq/dynamic}) are different solvers. +extended Lagrangian method ({qeq/dynamic} and {qeq/fire}) are +different solvers. -Note that the {qeq/point} and the {qeq/dynamic} styles both describe +Note that {qeq/point}, {qeq/dynamic} and {qeq/fire} styles all describe charges as point charges that interact through 1/r relationship, but -solve partial charges on atoms using different solvers. Styles -{qeq/point} and the {qeq/dynamic} should yield comparable results if +solve partial charges on atoms using different solvers. These three +styles should yield comparable results if the QEq parameters and {Nevery}, {cutoff}, and {tolerance} are the -same. Style {qeq/point} is typically faster, but {qeq/dynamic} scales -better on larger sizes. +same. Style {qeq/point} is typically faster, {qeq/dynamic} scales +better on larger sizes, and {qeq/fire} is faster than {qeq/dynamic}. NOTE: To avoid the evaluation of the derivative of charge with respect to position, which is typically ill-defined, the system should have a zero net charge. NOTE: Developing QEq parameters (chi, eta, gamma, zeta, and qcore) is -an "art". Charges on atoms are not guaranteed to equilibrate with +non-trivial. Charges on atoms are not guaranteed to equilibrate with arbitrary choices of these parameters. We do not develop these QEq paramters. See the examples/qeq directory for some examples. @@ -193,3 +212,6 @@ Chemistry, 95, 3358-3363 (1991). :link(vanDuin) [(ReaxFF)] A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J Physical Chemistry, 105, 9396-9049 (2001) + +:link(Shan) +[(QEq/Fire)] T.-R. Shan, A. P. Thompson, S. J. 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5,361,362,363,365,366,367,370,395,416,417,424,466,467,469,471,472,474,477,479],affin:[16,17,18,220,370,386],afil:233,aforement:18,afresh:[287,477,495],afshar:391,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,146,147,148,149,150,151,152,155,156,157,158,160,161,168,169,171,172,175,176,181,190,191,192,193,194,195,197,198,199,203,204,206,207,214,215,216,217,218,220,224,231,242,243,244,245,246,251,252,253,255,261,262,263,269,274,275,276,278,281,285,289,297,299,302,310,315,317,318,319,321,322,323,324,325,329,331,333,337,340,341,347,354,360,361,363,364,366,368,369,370,371,372,377,384,386,393,394,395,396,402,403,404,415,416,417,419,420,421,422,426,430,432,433,440,441,451,453,454,455,458,464,466,468,469,470,471,472,474,475,477,479,481,483,486,487,490,494,495,496,497,498,499],afterrun:477,afterward:3,afterword:41,ag1:167,ag2:167,again:[6,11,12,16,17,62,142,148,154,162,191,194,220,235,285,340,354,365,416,417,464,466,467,469,471,476,483,485,495,497],against:[11,12,13,64,221,365,432,433],aggreg:[6,12,65,68,69,79,93,110,117,235,251,297,299,312,464,496],aggress:[235,483],agilio:[9,13],agre:[3,8,188,363,372,404,433],agreement:[5,7],ahd:401,ahead:333,aidan:[0,5,7,9,13,358],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:193,akohlmei:[7,9,13,195,236],aktulga:[7,9,292,433],al2o3:440,al2o3_001:[120,300],al3:167,ala:[242,440],alain:9,alat:[280,419],alb:[430,453,455],albeit:298,albert:9,alchem:[87,162],alcohol:329,alcu:[371,377],alcu_eam:430,alderton:390,alejandr:[255,256],alessandro:13,algebra:422,algorithm:[0,1,6,7,8,9,41,61,194,203,214,217,220,242,244,245,269,282,299,302,321,322,326,329,334,361,362,363,367,370,395,417,422,437,439,464,466,483],alia:[12,16],alias:[1,356],aliceblu:194,align:[6,12,29,41,71,170,188,210,214,237,358,469,472,490],alkali:395,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,156,161,162,163,164,165,166,167,168,169,170,171,172,174,176,181,187,188,191,192,193,194,195,197,198,199,200,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,223,224,225,226,227,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,248,250,251,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,272,273,274,275,276,277,278,279,280,281,282,284,285,286,287,288,289,290,291,292,294,295,296,297,298,299,300,301,302,303,304,305,306,310,311,313,314,315,316,317,318,321,322,323,324,325,326,327,328,329,331,332,333,334,335,336,337,338,339,340,341,345,350,353,354,355,356,357,358,360,363,364,365,366,367,369,370,371,372,373,375,376,377,378,380,381,382,383,384,386,387,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,415,416,417,418,419,420,421,422,423,424,425,426,427,429,430,431,432,433,434,435,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,461,462,463,464,466,467,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,484,486,487,488,490,494,495,496,497,498,499],allen:[29,87,390,398],allentildeslei:87,allign:3,allindex:338,alloc:[3,5,6,8,9,11,12,60,229,328,364,366,370,428,433,469,477],allocat:3,alloi:[],allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,92,108,110,144,146,147,148,161,166,167,168,170,176,187,188,191,193,194,195,197,198,200,202,203,204,206,207,208,209,210,211,212,214,216,217,218,219,220,221,225,226,229,231,232,233,234,236,239,242,245,246,250,252,255,256,280,284,286,287,288,289,293,299,300,302,303,305,306,310,314,321,322,323,324,326,327,328,329,330,331,337,339,341,350,355,356,358,363,364,365,366,369,370,373,377,378,379,380,381,382,387,393,395,399,400,401,402,407,411,416,417,422,424,430,433,434,437,439,440,449,459,461,464,467,469,471,472,473,474,475,476,479,481,482,483,486,487,495,496],almost:[2,3,12,60,237,289,326,356,367,370,449],alo:387,alon:[6,7,217,295,432,433,467],alond:13,along:[6,8,9,12,29,40,71,87,120,167,168,190,191,193,206,217,237,242,243,247,252,254,289,299,302,303,307,311,312,321,325,326,332,335,337,358,361,362,363,365,387,390,399,402,405,407,411,419,432,433,452,469,472,479,480,495],alonso:[420,421],alpha:[6,12,51,198,242,281,289,294,363,371,374,378,387,391,393,394,396,401,406,407,419,425,429,454,456,487,490],alpha_:[],alpha_c:415,alpha_i:441,alpha_ialpha_j:[],alpha_lj:415,alphabet:[2,3,22,37,44,55,63,176,187,197,341,350,364,384,450,469],alphanumer:[3,63,197,288,296,339,364,495],alreadi:[3,7,8,9,12,16,17,18,42,168,169,171,192,202,206,210,211,214,216,220,246,287,289,314,337,364,365,391,400,402,409,417,449,459,462,465,469,470,474,479,495],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,72,73,75,77,81,87,89,90,92,94,1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0,482],chipot:219,chiral:349,chmod:[11,12],cho:419,chocol:[7,194],choic:[3,6,12,15,16,18,40,41,54,87,143,146,147,161,172,188,206,210,211,214,217,220,221,233,239,242,253,255,282,290,299,321,350,356,361,362,365,367,370,402,415,424,428,469,478,479,482,483,489,490,494],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,119,158,159,193,215,216,217,218,221,228,239,242,253,255,257,258,259,260,261,262,263,286,314,318,332,355,356,362,459,464,466,478,484],chose:[453,455],chosen:[2,3,6,12,17,142,168,171,180,188,193,199,204,218,221,228,231,232,240,242,253,255,260,282,285,296,314,318,321,322,327,329,330,336,356,357,362,370,395,399,405,406,409,435,453,464,478,483,490],chri:166,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,94,105,107,116,148,163,165,206],chute:[4,10,234],ciccotti:302,cieplak:[6,174,481],cii:207,cij:207,circl:[42,71,310],circular:[3,6,146,189],circumst:18,circumv:[92,108,294],citat:[],cite:[3,7,8,12,239,440],ckio:2,cko:2,cl1:167,clarendon:[29,390],clarifi:[7,453,455],clariti:339,clark:427,class2:[],classic:[0,3,5,6,7,8,9,229,282,289,294,326,351,395],classifi:[9,450,458],claus:467,clean:[6,12,14,15,17,477],cleanli:[468,498],clear:[],clearli:7,clebsch:142,clermont:[9,13],clever:473,click:[2,11,22,37,44,55,168,176,187,193,236,341,350,365,384,450],client:[236,238],climb:[254,365,483],clinic:[7,13],clo:[157,190,496],clock:[12,464,483],clockwis:332,close:[3,6,11,12,13,39,41,67,143,171,191,216,217,218,233,240,242,255,276,299,302,332,335,354,356,359,361,362,365,370,372,377,387,388,419,424,436,438,455,473,479,490,492],closer:[3,41,118,166,190,191,214,218,222,323,365],closest:[216,280,299,329,398,434,449,459],cloud:[440,490],clovertown:18,clsuter:72,clump1:[284,299],clump2:[284,299],clump3:[284,299],clump:299,cluster:[],clutter:[3,9],cmap:469,cmatrix:233,cmax:419,cmd:[11,12,282,480],cmdarg:11,cmin:419,cmm:[],cn1:207,cn2:207,cna:[],cnn:207,cnr:[9,13],cnt:[402,473],co2:[40,167,302,364],coars:[7,9,29,36,40,54,180,284,299,314,400,435,481],coarser:[356,495],coarsest:142,code:[],coeff:[3,7,8,12,21,22,33,44,50,174,175,176,181,340,341,347,384,402,406,424,437,439,442,469],coeffcient:469,coeffici:[],coefficienct:391,coefficient0:393,coefficient1:393,coeffieci:[6,374],coeffincientn:393,coexist:[9,231,395],cohes:[6,396,419],coincid:[124,335,382,416,417,464],colberg:192,cold:[6,153,231,235,366,490],coldest:322,coleman8:9,coleman:[9,120,167,300],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,94,99,105,107,116,148,156,163,165,168,191,194,206,219,245,251,284,294,297,299,337,355,364,366,385,405,469,476,482,488,499],collid:[225,314,336],colliex:167,collinear:[3,284],collis:[3,242,314,332,336,392,399,462],colllis:314,colloid:[],colombo:39,colon:[195,337,470],color1:194,color2:194,color:[3,9,41,191,193,194,214,232,289,294],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,94,105,107,108,110,112,115,116,117,118,119,121,142,143,148,156,163,165,166,167,188,191,194,197,205,206,207,209,210,211,212,245,252,253,289,299,315,316,326,336,397,401,432,433,470,484,486,495],colvar:[],colvarmodul:12,com:[],comamnd:220,comand:217,comannd:370,comb3:[],comb:[],comb_1:291,comb_2:291,combiant:388,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,93,104,110,117,146,147,161,191,193,203,209,236,245,255,282,288,318,327,335,338,340,355,356,358,362,370,385,387,388,395,396,402,414,415,441,451,453,455,458,461,472,477,482,490,495],come:[],comfort:[12,13],comm:[0,3,11,12,61,73,192,236,238,239,356,365,370,391,424,429,452,471],comm_modifi:[],comm_modift:61,comm_styl:[],comm_world:11,command:[],comment:[2,7,11,12,38,56,174,188,191,240,299,326,364,365,371,393,394,396,406,419,426,433,440,441,451,452,453,454,455,458,466,467,469,490,495],commerci:7,commmand:[3,6,12,59,109,277,463,464,466,483,498],common:[],commonli:[3,6,12,17,25,57,59,106,108,170,191,193,195,351,400,409,441,453,455,469,472,481],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,171,172,193,194,214,215,216,218,219,220,236,238,242,244,245,246,255,281,288,290,291,292,299,314,326,337,353,355,366,367,368,370,392,428,466,467,478,479,495,497,499],communc:355,comp:[7,192,238,239,302,356,365,395,424,429,434,448,452,454],compact:[63,197,384,450],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,112,120,151,166,167,176,187,194,224,290,337,339,355,356,363,365,419,440,464,483,484,490,494],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,175,176,187,340,341,350,383,450],compat:[3,5,7,8,9,11,12,13,17,18,41,71,119,121,179,191,195,199,205,206,207,209,210,211,212,214,281,293,318,321,328,331,334,355,370,403,422,424,452,466,467,495],compens:[6,215,216,297,366,395],compet:325,competit:356,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,166,191,192,193,195,236,325,356,370,422,469,470,474,495],compl:17,complain:[12,17],complement:419,complementari:[7,387,407],complet:[3,6,9,11,12,15,41,59,71,194,210,214,219,245,282,285,288,314,325,327,339,354,365,370,396,437,439,457,464,469,474,477,481,483,486,490,495],complex:[6,8,11,12,13,25,40,42,62,92,108,142,144,156,168,169,242,310,335,353,365,395,422,452,467,469,472,495],compli:[321,325],complic:[6,7,9,12,13,204,231,467],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,92,94,95,98,105,106,107,108,109,110,111,112,114,115,119,129,132,133,134,135,138,139,140,142,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,161,163,164,165,190,191,193,194,200,201,205,206,207,208,209,210,211,212,213,217,218,220,221,226,229,234,238,239,242,245,247,251,252,254,255,256,260,261,262,263,274,275,276,278,279,281,282,283,286,297,299,301,302,303,307,308,311,314,317,318,319,321,328,329,334,335,336,355,358,362,363,364,365,370,376,391,395,399,416,417,437,439,440,441,469,470,479,487,495,496],componenet:6,composit:[6,204,242,393],compound:[386,395,396,458],compres:[71,116,206],compress:[],compris:[40,335,405,434,457],compton:[120,167],comptu:3,compuat:356,comput:[],computation:[3,6,215,216,326,377],computational:490,compute_arrai:8,compute_fep:[199,415],compute_group_group:231,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[120,300],compute_scalar:8,compute_temp:8,compute_ti:199,compute_vector:8,compute_xrd:167,concaten:[2,3,498],concav:335,concentr:[71,393],concept:[6,148,158,206,478],conceptu:[3,6,71,156,218,220,365,387,402,419,474],concern:[6,73,87,192,232],concetr:71,concis:[11,325],conclud:12,concret:8,concurr:[9,16,356,495],conden:[326,453,455],condens:[6,150,326,372,389,393,407,458],condit:[],conducit:6,conduct:[],cone:472,confer:422,confid:[3,483],config:[12,191,466],configfil:219,configur:[1,2,6,12,15,17,38,59,124,170,188,190,191,193,197,218,219,220,221,225,231,238,239,269,282,290,325,353,363,365,372,377,394,419,422,451,453,455,458,464,469,471,472,483],confin:[469,483],conflict:[3,12,40,424,467],conform:[3,6,13,59,217,218,254,298,303,325,349,365,395,481],confus:[3,458],conjuct:391,conjug:[7,8,239,362,395,432,433],conjunct:[6,7,71,86,87,116,151,156,162,168,172,194,198,199,239,242,246,269,285,286,290,291,292,294,299,314,322,329,334,355,356,365,378,380,384,387,391,395,401,407,424,427,435,456,469,472,476,490,499],connect:[3,6,87,153,171,217,236,284,299,302,311,365,388,399,449,455,466,467,473,490],conput:3,consecut:[3,11,12,39,71,168,194,198,199,221,236,237,387,407,411,464,470,472],consequ:[1,6,204,326,406,483],conserv:[3,29,197,204,217,224,225,232,235,239,241,242,246,251,253,255,269,299,302,317,318,322,329,330,334,365,390,391,399,413,440,478,483],consid:[6,9,70,71,78,87,117,150,153,154,171,191,194,198,199,205,207,210,214,216,217,221,243,256,281,299,321,322,325,326,329,356,384,395,402,433,434,440,449,464,465,467,470,471,472,474,477,479,487,490,495],consider:[6,8,239,240,317,318,319,370,478],consist:[3,6,8,9,11,12,40,42,65,69,79,93,105,110,113,114,117,148,151,153,168,180,190,195,200,201,206,220,221,224,226,229,232,239,240,241,252,255,257,258,259,260,261,262,263,264,265,267,268,269,270,272,273,274,275,276,277,278,286,289,294,296,298,299,317,318,319,320,330,355,356,358,364,365,370,372,377,379,385,387,395,398,402,416,417,419,422,424,434,437,439,440,452,459,467,469,470,471,472,473,474,481,490,495],consistent_fe_initi:203,consit:299,constant:[],constitu:[3,6,245,299,331,335,385,434],constitut:[437,439],constrain:[3,6,8,145,146,147,148,149,151,154,155,156,157,158,160,161,197,206,221,231,232,237,245,249,284,285,297,299,302,312,322,329,363,364,395,474,481,490],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,92,108,120,142,167,218,255,281,298,335,366,370,390,422,424,449,451,452,472,473,488,495],constructor:[8,11],consult:433,consum:[1,294,428,495],consumpt:353,contact:[],contact_stiff:[436,438],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,118,120,142,148,156,166,167,168,170,174,176,187,188,191,193,194,195,197,198,199,203,205,206,207,209,210,211,212,214,219,221,226,233,237,238,239,242,253,269,280,281,284,285,287,289,292,296,299,300,304,314,321,325,326,335,336,339,354,356,364,365,368,369,371,372,373,377,386,387,390,393,394,395,402,403,419,422,426,430,431,432,433,441,451,452,453,454,455,456,458,464,465,466,467,469,470,471,472,474,476,478,481,483,486,487,490,495,497,499],content:[12,18,433,485,487],context:[3,6,8,12,17,118,119,194,215,216,221,284,296,330,362,461,469,476,485,494,495,496],contibut:70,contigu:466,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,104,105,164,194,197,198,199,204,206,207,208,209,210,211,212,214,217,218,219,220,221,231,232,233,235,236,237,239,240,241,247,252,253,255,257,258,259,260,261,262,263,274,275,276,277,278,283,285,288,289,299,300,303,313,314,316,323,324,326,332,335,339,354,369,370,377,391,392,409,412,432,433,434,437,439,454,464,467,469,471,472,477,483,486,487,495,497],continuum:[6,7,9,203,326,437,439],contour_integr:203,contract:[59,218,220,255,286,299],contradictori:3,contrain:302,contraint:269,contrari:[233,240],contrast:[1,6,42,55,64,150,153,220,337,437,439,461,498],contrib:326,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,94,103,105,107,109,110,111,112,114,116,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,199,204,205,206,207,209,210,211,212,218,231,239,242,245,246,250,256,276,277,284,285,293,296,299,300,302,328,355,363,365,373,391,392,393,395,402,416,417,422,424,432,433,440,481,487,490],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,124,142,177,191,193,197,203,204,214,218,219,220,235,236,239,240,255,257,258,259,260,261,262,263,286,291,299,305,306,317,318,319,326,330,353,355,367,395,398,422,432,433,436,438,451,455,464,466,478,484,485],control_typ:203,controlfil:433,convect:91,conveni:[6,12,29,191,195,212,300,358,441,495],convent:[3,8,9,29,179,186,187,194,298,311,338,393,395,495],converg:[3,6,41,88,191,193,195,200,214,217,218,226,229,260,289,291,294,298,302,361,362,363,365,386,387,407,440,464,476,483],convers:[3,8,142,193,194,204,207,286,355,387,388,389,395,407,411,415,427,467,483,494],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,168,175,191,193,194,212,253,337,340,342,346,349,358,365,371,393,422,453,455,462,467,469,470,471,476,486,490,494,495,497,499],convex:[42,335,376],convinc:[7,12],cook:9,cooki:7,cool:[7,158,235,297],cooordin:191,cooper:[5,7],coord123:116,coord1:[3,116,206,210,211],coord2:[3,116,206,210,211],coord3:[3,116,206,210,211],coord:[],coordb:440,coordbb:440,coordiat:363,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,94,104,105,107,115,116,118,136,142,151,157,163,165,166,168,172,190,191,192,193,194,195,197,200,205,206,209,210,211,214,215,216,217,218,219,220,221,224,226,227,229,231,234,235,236,237,238,239,240,252,254,255,257,258,259,261,262,263,276,279,280,281,284,285,286,296,297,299,301,302,303,308,311,312,313,314,316,324,325,326,333,334,336,337,358,363,364,365,370,371,372,375,376,394,440,464,469,470,471,472,474,477,479,483,490,495,496],coordn:[116,206],coorind:105,copi:[0,3,4,8,11,12,15,17,40,121,193,326,365,384,432,467],copper:462,coproccesor:16,coprocessor:[1,4,7,9,16,17,370,482],coproprocessor:17,copy_arrai:8,copyright:[7,8,284],coral:194,core:[],core_shel:150,coreshel:[6,9,380,387,389],cornel:[6,174,481],corner123i:115,corner123x:115,corner123z:115,corner1i:115,corner1x:115,corner1z:115,corner2i:115,corner2x:115,corner2z:115,corner3i:115,corner3x:115,corner3z:115,corner:[3,6,40,115,193,335,336,358,457,469],cornflowerblu:194,cornsilk:194,corpor:16,corr:386,correct:[3,6,9,11,12,16,17,59,87,88,103,104,112,118,150,155,162,193,220,231,233,239,255,256,276,284,286,289,325,331,335,355,365,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,457,458,460,461,462,469,484,487,490],correction_max_iter:203,correctli:[3,8,9,11,17,71,81,103,104,145,146,147,149,151,153,154,155,156,157,160,161,164,191,194,200,221,226,229,240,249,255,256,292,299,302,311,313,332,335,365,366,370,389,417,422,466,467,469,479,494,496],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,87,97,98,111,114,115,116,117,120,121,129,132,133,134,135,136,138,139,140,142,145,146,155,162,167,174,175,176,177,178,179,180,182,183,185,186,188,191,193,194,198,199,200,206,208,209,210,211,213,216,218,220,227,229,230,234,239,242,243,251,252,253,255,257,258,259,260,261,262,263,264,265,269,272,274,275,276,278,281,282,286,291,299,301,302,317,319,321,330,331,332,334,335,336,338,340,341,342,343,345,346,349,351,356,360,362,364,365,371,372,374,378,379,380,381,382,383,384,385,386,387,390,391,393,394,395,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,419,420,422,424,425,426,427,429,430,432,433,434,435,440,441,442,451,452,453,454,455,457,458,460,461,462,464,466,467,469,470,472,482,483,484,486,487,490,495],correspondingli:[416,417,478],cosin:[],cosineshift:27,cosmo:[233,238],cossq:[],cost:[1,6,10,11,12,17,39,41,71,111,120,143,167,193,194,206,210,211,214,215,216,228,255,291,326,355,356,368,387,407,411,422,424,451,466,478],costheta0:[451,453,455,458],costheta:430,costli:[11,88,233,366],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,94,105,107,111,114,116,148,158,163,165,181,191,193,194,198,199,206,207,210,214,220,229,238,288,289,290,294,297,299,301,314,315,321,325,326,327,331,335,337,339,347,352,354,361,363,366,370,373,397,401,402,432,433,465,466,467,469,471,473,476,477,485,490,495,496],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,88,109,110,118,143,169,173,290,292,327,355,356,363,370,378,380,381,382,383,386,387,388,389,390,395,399,400,402,407,411,415,418,424,427,432,433,435,440,450,455,456,458,461,474,481,487,490,494],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,116,118,119,156,166,172,200,201,204,206,209,210,211,213,214,221,226,228,231,237,255,269,285,302,317,318,335,356,363,364,365,367,370,397,401,424,487,495],counter:[332,464,475,477,483],counteract:231,counterbal:235,counterbalanc:29,counterpart:[191,299,464],counterproduct:18,coupl:[],courant:304,cours:[3,8,128,130,162,191,198,199,232,298,311,325,331,333,334,336,337,356,416,442,466,469,482,490,495,497],courtesi:358,cov:440,coval:[6,29,395,419,440,490],covari:233,cover:[6,71,188,194,203,242,395,405,457],coverag:[71,210],cpc:238,cpp:[1,3,6,8,9,11,12,13,87,191,198,199,229,302],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,194,208,224,240,327,353,356,370,384,450,464,482,483,486,487,488,495],cpuremain:487,cr2:167,cr3:167,crack:[4,366],crada:[5,7],crai:[5,7,13,18,191],crash:[3,12,366,490],craympi:370,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:203,create_faceset:203,create_group:192,create_nodeset:203,createatom:[],creation:[],crimson:194,critchlei:284,criteria:[3,118,169,193,194,215,216,217,250,363,429,457,471,474,495],criterion:[12,41,123,166,168,171,204,214,217,231,269,291,304,332,337,363,365,386,395,399,440,474,483,484],criterioni:483,critic:[6,48,49,253,321,326,363],crmax:71,crmin:71,cross:[3,12,22,71,89,146,176,191,193,205,210,216,220,252,254,276,299,307,311,313,322,329,341,358,365,382,391,392,393,400,401,402,407,409,411,430,435,437,439,453,455,462,469,473,479,497],crossov:1,crossterm:469,crozier:[0,7,13],crucial:289,crystal:[4,6,13,73,108,280,281,324,358,366,473,487,490],crystallin:[6,104,281,358,454,490],crystallis:321,crystallogr:[120,167],crystallograph:[358,487],crystallographi:[120,167,358],cs1:167,cs_chunk:6,cs_im:[40,469],cs_re:[40,469],csanyi:[142,431,441],cscl:419,csequ:6,csh:[11,12,384],cshrc:[11,12],csic:[394,451,453,455,458],csinfo:6,csisi:[394,451,453,455,458],csld:[],cst:393,cstherm:6,cstyle:466,csvr:[],ctcm:[371,393],ctemp_cor:224,cterm:303,ctr:9,ctype:11,cu1:167,cu2:167,cu3au:419,cube:[6,41,166,171,214,224,335,358,490],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:377,cummul:[3,6,212,215,216,217,219,228,233,239,241,314,317,318,319,320,322,329,401,487],cumul:[6,204,206,209,210,211,225,231,239,253,255,260,269,299,300,365],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,103,104,110,118,119,132,143,148,156,158,164,166,169,172,190,191,192,193,194,195,198,199,203,206,210,211,212,214,215,216,217,218,219,220,221,225,226,229,231,233,236,237,239,245,252,255,256,261,262,263,269,274,275,276,278,284,290,291,293,296,297,298,299,302,303,304,305,306,307,308,310,312,313,314,317,318,319,325,326,329,330,331,332,333,334,336,337,339,353,354,355,356,359,360,362,363,364,365,370,376,377,384,386,390,393,395,396,399,402,403,406,416,417,419,420,421,424,430,432,433,436,437,438,439,442,453,455,456,459,464,465,466,467,469,470,471,472,473,475,476,477,479,481,483,484,486,487,495,496,497,498,499],curv:[6,168,231,281],curvatur:[398,434,462],custom:[],cut0:467,cut1:478,cut2:478,cut:[],cuthi:[280,292],cutinn:[379,416,417],cutlo:[280,292],cutmax:430,cutoff1:[383,390,407,411,415,418,427,435],cutoff2:[378,380,381,383,389,390,407,411,415,418,427,435],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,92,108,110,117,118,142,166,169,171,216,217,222,280,289,290,292,294,296,299,314,327,331,335,337,353,355,356,363,366,367,368,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,387,388,389,390,391,392,393,394,395,396,397,398,400,401,402,403,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,432,433,434,435,440,441,442,443,444,445,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,467,471,474,478,490,495],cutoff_glob:376,cutoff_inn:376,cutoffa:394,cutoffc:394,cuu3:393,cval:167,cvd:321,cvel:303,cvff:[],cwiggl:[3,252,331,334,336,495],cyan:[2,193,194],cycl:[3,231,253,255,256,260],cyclic:[3,188],cygwin:12,cylind:[3,4,71,193,206,237,285,332,335,472],cylindr:[6,237,311,332],cypress:370,cyrot:377,cyrstal:281,d3q15:242,d3q19:242,d_double_doubl:15,d_e:326,d_flag2:288,d_flag:288,d_name:[115,191,288,316,479],d_single_doubl:15,d_single_singl:15,d_sx:288,d_sy:288,d_sz:288,daan:324,dai:12,daili:12,daivi:276,damag:[],dammak:294,damp:[3,6,197,202,239,240,241,246,255,256,260,286,289,294,299,317,318,330,332,333,362,363,365,378,380,382,387,390,395,399,407,415,427,435,450,456,483,490],damp_com:240,damp_drud:240,dampen:[299,490],dampflag:[332,399],dan:17,danger:[3,12,231,337,391,487],dangl:171,daniel:9,darden:[356,390],darkblu:194,darkcyan:194,darken:193,darkgoldenrod:194,darkgrai:194,darkgreen:194,darkkhaki:194,darkmagenta:194,darkolivegreen:194,darkorang:194,darkorchid:194,darkr:194,darksalmon:194,darkseagreen:194,darkslateblu:194,darkslategrai:194,darkturquois:194,darkviolet:194,dasgupta:290,dash:[399,486],dat:[6,91,188,203,465],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,300],dataset:300,datatyp:3,date:[0,6,12,13,190,432,433,495],datom1:117,datom2:117,datom3:117,datom4:117,datum:[3,6,42,65,68,69,79,93,110,117,191,207],davenport:418,davi:331,david:[9,19,355,356,453,455],daw:[393,430],dbg:14,dcd:[3,6,7,191,192,193,194,195,282,470,474],ddim:190,deactiv:415,dealt:238,debug:[6,7,11,12,13,14,17,120,124,167,168,282,287,353,355,370,403,424,459,467,468,476,479,486,495],deby:[],decai:[92,387,462],decid:[3,6,12,16,71,252,288,299,327,484],decipher:358,declar:192,declin:314,decod:193,decompos:[87,441],decomposit:[3,5,7,18,62,203,282],decoupl:[6,490],decreas:[3,191,200,201,208,217,220,226,229,231,239,325,355],decrement:303,deepli:352,deeppink:194,deepskyblu:194,def:[12,13,467],defaul:61,defect:[6,70,166,422],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,174,175,176,177,178,179,180,182,183,185,186,187,188,189,190,191,192,193,194,197,198,199,200,201,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,220,221,224,225,226,229,230,231,234,237,238,239,240,241,242,250,252,254,255,256,257,258,259,260,261,262,263,265,266,267,270,272,273,274,275,276,277,278,280,281,282,284,285,286,288,290,292,297,299,300,301,302,304,308,312,314,316,317,318,319,320,322,323,324,326,328,329,331,332,333,334,335,336,337,339,340,341,342,343,344,345,346,349,350,351,353,355,356,358,360,362,363,364,365,366,367,368,369,370,372,373,374,375,376,378,379,380,381,382,383,384,385,387,388,390,391,392,394,395,397,398,399,400,401,402,403,405,407,408,409,410,411,412,413,414,415,416,417,418,422,423,424,425,426,427,429,430,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,466,467,469,470,472,473,474,475,478,479,480,481,483,484,486,487,490,491,492,493,494,495,496],definit:[2,3,6,8,12,13,78,80,118,142,194,206,207,208,209,210,211,212,220,237,260,300,316,328,331,334,336,338,350,353,364,373,377,385,395,405,430,437,439,441,457,467,469,471,478,480,494,495],defint:487,deform:[],deg2theta:167,deg:490,degener:[3,284],degrad:[8,18,281,356,478],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,93,95,97,98,100,102,103,108,114,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,161,167,168,174,175,178,179,186,188,190,193,206,217,224,231,233,234,239,240,245,255,256,260,261,262,263,274,275,276,278,282,284,298,299,302,317,318,319,324,340,342,346,349,351,363,390,393,401,479,487,490,496],degress:[148,206],del:483,delai:[3,6,12,366,392,487],deleg:402,delet:[2,3,7,8,12,54,57,60,63,166,171,172,197,206,207,209,210,211,212,215,217,228,231,255,300,317,318,337,339,354,364,366,369,424,449,469,470,471,472,480,481,486,491,493,495,496],delete_atom:[],delete_bond:[],delete_el:203,deli:190,delimit:[467,495],deloc:[256,395,440],delr:419,delt_lo:483,delta:[],delta_1:377,delta_3:377,delta_7:377,delta_conf:3,delta_ij:[419,430],delta_mu:3,delta_pi:377,delta_r:430,delta_sigma:377,delta_ua:376,delx:190,delz:190,dem:376,demand:294,demo:11,demon:279,demonstr:[289,419],den:285,dendrim:401,denniston:[9,242,244,245,246,281],denomin:[7,173],denot:[120,224,240,281,292,294,387,400,402,433,437,439],dens:[71,217,395],densiti:[3,6,7,9,18,40,41,59,101,118,128,142,154,166,168,198,199,203,206,210,211,214,220,229,242,245,248,249,281,285,286,290,326,331,358,360,364,371,377,393,419,420,421,430,434,440,444,446,447,448,469,478,479,487,494],density_continu:439,density_summ:439,depart:[0,7],departur:[253,289],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,93,104,110,111,114,115,116,117,121,142,145,151,155,156,162,168,169,174,175,176,177,178,179,180,182,183,185,186,187,188,190,191,193,194,197,198,199,200,201,204,206,208,209,210,212,213,214,216,218,220,226,227,230,233,234,235,237,239,240,242,244,245,252,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,280,291,294,296,299,301,302,308,314,317,318,319,321,323,325,326,328,330,331,334,335,336,337,339,340,341,342,343,345,346,349,351,356,358,363,364,366,367,368,370,371,372,374,375,377,378,379,380,381,382,383,384,385,386,387,388,390,391,393,394,395,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,419,420,422,423,425,426,427,429,430,432,433,434,435,440,441,442,450,451,452,453,454,455,456,457,458,460,461,462,464,466,469,471,472,475,479,481,483,486,487,489,495,496],dependend:6,depflag:12,dephas:[464,483],depos:221,deposit:[],deprec:[290,432],depth:[51,146,193,326,398,434],dequidt:9,der:[87,109,385,386,415,432,433,461,490],deriv:[6,7,8,9,38,56,63,87,142,162,188,207,218,220,231,239,252,255,257,258,259,260,261,262,263,280,286,290,294,323,324,326,331,332,335,362,364,372,377,385,390,395,396,400,409,413,414,419,422,432,433,450,452,461,490],derjagin:461,derlet:280,descend:194,descent:[7,362],descib:[40,193,290],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,112,115,118,120,132,142,143,146,147,148,152,153,156,159,161,162,166,167,168,170,171,180,185,188,191,192,197,198,199,206,207,208,209,210,211,212,214,217,218,219,220,221,223,224,232,233,236,237,238,239,240,241,242,244,245,246,250,254,255,256,260,268,277,280,282,287,288,289,290,291,292,299,303,311,314,315,316,317,318,319,320,321,322,323,324,329,331,332,334,339,355,356,358,361,362,363,364,365,369,372,373,375,376,378,379,380,382,383,384,385,386,387,390,393,395,396,398,399,400,402,407,408,409,410,411,412,413,414,415,416,417,418,419,422,423,429,430,431,432,433,434,435,440,441,442,449,450,451,452,453,454,455,456,458,460,461,462,464,466,467,469,470,471,472,473,479,482,483,486,495,496,497],descript:[],descriptor:[142,191,403],deserno:356,design:[0,3,6,7,8,9,11,13,14,15,17,120,150,153,167,203,217,223,224,255,256,280,281,300,321,326,373,374,375,376,379,382,387,389,395,415,416,417,420,421,430,433,452,478],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,114,119,143,150,168,181,190,206,212,218,220,229,231,232,239,240,241,245,255,276,284,285,286,287,290,294,299,302,314,317,318,319,320,325,332,347,352,355,356,358,361,363,364,365,391,393,401,416,417,451,453,455,465,466,467,469,473,478,483,484,486,487,495,496,497],desk:7,desktop:[4,6,7,10,12,193],despit:490,destabil:377,destre:349,destroi:[11,39,215,216],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,94,103,105,107,109,111,113,114,116,119,121,142,143,145,146,147,148,151,161,162,163,165,168,169,172,173,176,187,190,191,193,194,197,198,199,203,206,207,208,209,210,212,214,216,217,218,219,220,221,229,231,232,233,234,236,237,239,241,242,246,252,253,254,255,256,257,258,259,260,261,262,263,267,269,274,275,276,277,278,281,284,285,286,288,289,291,292,293,299,302,314,317,318,319,320,321,322,324,325,326,327,328,329,330,337,339,341,350,355,356,359,363,364,366,367,370,371,372,373,375,376,377,379,381,382,383,384,385,386,387,390,391,395,396,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,417,418,419,423,424,429,432,433,434,440,441,442,450,457,460,461,467,469,470,471,472,474,475,478,479,481,484,487,488,495,496,499],detect:[2,3,12,42,61,63,86,92,230,285,325,365,386,401,406,464,466,469,480,483,495],determ:370,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,87,103,109,111,114,120,121,129,143,156,157,166,167,168,190,191,193,194,195,196,200,201,202,205,206,207,208,209,210,211,212,213,214,218,220,221,224,226,231,234,235,237,239,240,245,250,252,253,255,261,262,263,274,275,276,278,280,282,286,289,296,297,298,299,300,301,304,306,308,314,317,318,319,321,327,328,331,332,333,334,335,336,337,350,355,356,358,364,366,367,370,372,373,381,386,390,392,393,397,399,402,403,411,419,422,424,433,434,440,449,452,456,461,466,469,470,472,474,476,479,483,485,486,488,494,495,496],detil:110,devan:[9,435],devanathan:455,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,236,260,284,289,290,293,372,377,395,421,422,440,458,471],devemi:9,deviat:[253,260,280,397],deviator:9,devic:[1,3,12,15,17,236,370],device_typ:370,devin:[291,386],devis:421,dfactor:193,dff:490,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,356],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,293,422],dhi:[59,190,220,285],dhug:[253,289],dhugoniot:[253,289],dia:419,diagnost:[],diagon:[3,6,83,142,143,144,218,255,286,299,329,437,439],diagonalstyl:441,diagram:[41,120,167,187,214,282],diallo:401,diam:[193,194,285,364],diamet:[3,6,40,42,115,168,191,193,194,198,199,239,285,299,314,330,332,364,376,385,398,399,405,409,434,457,461,469,470,479],diamond:[358,395,419],diamter:[40,285],dick:6,dicsuss:252,dictat:[204,253],did:[3,12,363,391,392,393,399,424,453,455,477],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,164,328,355],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,92,95,97,98,122,142,145,146,147,148,149,151,154,155,156,157,158,160,161,162,168,169,171,176,187,188,190,191,193,194,197,199,202,204,206,209,214,215,216,217,218,219,220,224,230,231,232,233,234,235,236,239,240,242,252,255,256,257,258,259,261,262,263,265,267,270,272,273,274,275,278,280,282,284,286,289,290,291,294,297,299,302,303,311,312,314,317,318,319,322,323,324,326,329,330,331,332,335,339,340,350,352,354,355,356,358,359,361,362,364,365,367,368,369,370,371,372,377,381,382,384,385,386,391,393,395,398,399,400,402,405,407,408,410,411,418,419,420,421,423,424,426,430,432,433,434,435,436,437,439,440,441,442,450,451,452,453,455,457,458,461,463,464,466,467,469,471,472,473,474,477,478,479,481,483,484,486,487,488,490,494,495,496,497],differenti:[1,3,6,29,188,355,387,430,454],difficult:[218,282,370,401,478],difficulti:[92,108,302,432],diffract:[],diffus:[],digit:[2,3,194,339,422],dih_table1:188,dih_table2:188,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:216,dihydrid:395,dij:302,dilat:[],dim1:3,dim2:3,dim:[3,59,71,145,149,150,151,154,155,156,157,158,160,168,190,210,220,237,332,358,419,472,494,495,496],dimdim:495,dimems:281,dimens:[],dimensinon:71,dimension:[3,39,92,114,120,142,145,148,149,150,151,154,155,156,157,158,160,167,189,206,210,254,281,326,358,361,365,430,469,479],dimensionless:[106,123,124,126,129,131,133,138,142,326,356,441,461],dimentionless:137,dimer:[6,299,419],dimgrai:194,dimstr:[41,214],dinola:[286,317],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,191,316,490],dir1:480,dir2:480,dir:[1,3,4,8,9,11,12,253,280,289,313,430,432,433,467,480,495],dirac:142,direc:430,direct:[],directli:[3,6,8,9,11,12,87,115,142,144,191,192,193,200,226,233,237,242,281,300,318,330,332,333,334,335,358,362,370,371,372,378,380,381,387,390,393,395,407,411,424,427,435,449,467,479,480,481,487,495],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,195,219,238,284,290,293,310,314,323,324,365,369,371,372,377,384,386,387,393,394,396,403,404,415,419,420,421,422,426,430,431,432,433,440,441,451,453,454,455,458,467,469,470,471,480,495],disabl:[3,12,16,326,406,467,482,495],disadvantag:[6,214],disallow:[191,220,255],disappear:471,discard:[2,3,41,71,208,210,214,327,335,466,471,472],discontinu:[9,188,363,413],discourag:419,discov:[13,327],discret:[6,8,40,42,193,194,239,242,376],discuss:[],disk:[6,84,85,92,161,189,221,231,285,467],disloc:[70,422],disord:[39,70,422],disp:[],dispar:434,disperion:[390,411],dispers:[3,6,7,9,166,281,355,356,381,390,411,416,424,433,452,458],displac:[],displace_atom:[],displace_box:59,displacemet:472,displai:[11,13,22,37,44,55,176,187,191,193,341,350,384,450],dispters:3,disregard:422,dissip:[6,232,239,281,323,324,379,391,399,416,417,450],dissolut:215,dist:[6,69,91,110,119,191,282,298,392,449,464,496],distanc:[],distinct:[6,224,296,355,434],distinguish:[6,86,142,245,376,395,468],distort:371,distrbut:371,distribut:[],distro:[113,384,429,430],ditto:[8,12,14,15,16,17,18,42,117,216,462,467],div:8,divd:119,diverg:[3,12,39,299,324,471,490,497],divid:[3,6,16,41,91,114,119,128,130,143,165,166,176,187,194,206,207,209,214,220,280,322,329,334,355,363,365,396,433,440,458,478,486,495],divis:[6,242,377,405,415,466,487,495],dl_poli:[6,7],dlambda:162,dlammps_async_imd:236,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,193],dlammps_gzip:[3,12,191,193,325,469,470,474],dlammps_jpeg:[3,12,193],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,193],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,191],dlen:479,dlmp_intel_offload:[12,16],dlo:[59,190,220,285],dlopen:6,dlvo:[7,385,461],dm_lb:242,dmax:[314,361],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,94,103,105,106,107,109,111,113,114,116,119,121,143,146,147,148,161,163,165,168,169,170,176,187,190,191,192,193,194,195,197,198,199,204,205,206,207,208,209,210,211,212,221,231,239,240,250,255,256,261,262,263,267,274,275,276,277,278,285,288,299,311,314,317,318,319,328,332,335,337,339,341,350,354,363,364,365,370,371,372,375,376,384,386,387,393,394,396,401,402,404,405,419,420,421,424,426,429,430,431,441,450,451,453,455,457,458,467,469,470,471,472,474,477,478,479,486,487,495,496,497,498],docuement:434,dodd:[42,376],dodgerblu:194,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,39,41,42,50,54,56,59,62,63,67,70,71,72,87,88,91,105,112,118,119,120,144,146,148,150,151,156,158,162,167,168,169,170,172,174,176,181,187,188,190,191,192,193,194,197,203,204,206,210,213,214,216,217,218,220,224,226,228,231,232,235,237,239,240,242,245,251,255,256,257,258,259,261,262,263,274,275,276,277,278,286,287,288,292,294,297,299,314,317,319,321,322,326,329,330,331,334,335,336,337,342,343,344,346,347,349,354,355,356,357,358,364,365,366,371,372,373,374,375,376,377,379,381,382,383,385,386,387,388,390,391,392,393,394,395,397,398,399,400,402,403,404,405,406,409,410,412,413,414,416,417,419,420,421,422,424,430,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,456,457,458,460,461,462,464,465,466,467,469,470,471,472,473,476,477,479,480,481,482,483,486,487,490,495,499],doegenomestolif:7,doesn:[3,7,8,12,168,191,204,210,211,311,364,366,370,372,386,394,404,432,433,451,453,454,455,458,469,471],dof:[3,8,114,146,147,148,161,206,299,496],dof_per_atom:[148,206],dof_per_chunk:[148,206],doff:[364,469],doi:[6,219],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,120,157,167,170,190,192,193,194,197,204,214,218,220,221,235,238,242,255,256,282,294,299,326,331,332,355,356,365,370,392,424,464,466,469,473,486],domin:[1,395,483],don:[0,8,11,12,13,118,171,200,226,240,288,335,419,440,467,469],donadio:318,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,162,165,168,171,188,191,193,194,203,204,206,208,209,210,211,212,214,215,216,217,218,220,221,229,231,236,237,239,240,247,255,261,262,263,274,275,276,278,279,281,282,283,288,296,299,300,302,314,317,318,319,321,323,324,337,339,354,355,356,363,365,366,369,370,372,381,393,402,403,404,411,417,418,419,424,432,449,452,457,464,465,466,467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,331,334,336,337,339,354,358,363,365,366,367,369,370,386,391,397,398,401,416,422,423,430,432,433,434,436,437,438,440,441,442,452,457,458,462,465,466,467,469,471,472,476,477,480,483,485,487,495,496],equat:[3,6,7,8,9,91,108,114,120,167,176,187,197,218,224,225,233,239,240,242,245,253,254,255,256,260,276,280,282,289,290,294,302,314,322,326,329,331,332,334,336,349,355,356,385,390,391,395,396,399,404,416,417,419,424,434,437,439,444,445,447,448,462,490],equi:256,equidist:254,equil:[3,290,359,476,499],equilater:479,equilibr:[3,4,5,6,7,9,59,91,168,197,204,207,217,218,231,253,255,256,276,277,289,290,291,292,322,323,324,329,386,387,432,433,465,479],equilibria:329,equilibribum:[215,216],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,151,152,175,177,218,220,231,232,233,240,242,255,260,276,289,294,298,302,303,311,314,321,322,324,329,340,342,346,349,386,419,426,440,490],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:203,equival:[6,12,13,29,59,61,126,127,135,140,166,170,194,209,212,218,220,231,239,255,276,286,298,299,334,391,395,440,453,455,469,472,477,478,487,490],equlibrium:6,equliibr:[290,292],er3:167,eradiu:[40,115,395,469],eras:[301,323],erat:[220,417],erc:387,erfc:[387,407,424],erforc:115,erg:494,erhart:[204,393,453,455],ermscal:373,ernst:9,eror:3,eros:419,erose_form:419,erot:[],errata:[453,455],erratum:331,erron:3,error:[],erta:399,ervel:[115,469],escap:[221,490],especi:[8,11,16,156,168,197,204,214,231,289,294,297,298,370,466],espresso:[9,293],essenti:[8,11,12,27,88,130,149,150,151,154,155,156,157,158,160,177,207,260,281,330,356,372,387,407,455,474,487],essex:29,establish:[87,235],estim:[1,3,6,10,12,38,41,56,91,143,203,214,225,253,314,321,355,356,361,424,433,452,483,487],esu:494,esub:419,eta:[6,242,255,289,290,292,330,394,396,398,430,454,458,494],eta_dot:255,eta_ij:430,eta_ji:396,etag:[40,469],etail:487,etap:255,etap_dot:255,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,95,111,112,115,117,143,145,148,149,150,151,152,154,155,156,157,158,160,162,168,170,171,172,181,191,193,194,197,198,203,204,205,206,209,210,211,212,215,216,220,221,229,231,232,239,255,285,296,300,326,327,335,339,354,355,363,364,365,366,368,393,394,402,415,417,422,428,432,433,451,453,455,458,464,467,469,470,471,476,478,479,483,485,486,487,488,490,494,495,497,499],ethernet:18,etol:[363,365,464,483],etot0:289,etot:[6,95,97,98,112,143,154,194,224,240,253,289,486,487],eu2:167,eu3:167,euler:[363,365],eulerian:203,euqat:443,europhi:242,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,87,88,91,109,119,142,144,148,158,166,168,190,191,193,194,198,199,200,201,203,205,206,207,208,209,210,211,212,213,220,226,232,234,235,237,238,239,240,281,287,290,301,304,308,317,318,319,328,331,334,336,337,339,355,356,361,363,370,422,424,430,436,438,440,452,464,465,467,471,472,474,476,477,478,479,483,485,487,495,496],evalut:[339,467],evan:[156,276],evanseck:[6,20,174,382,481],evapor:[],evaul:[8,363],evdwl:[109,432,433,487],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,121,169,170,184,188,191,194,197,198,199,204,205,206,209,210,211,212,214,215,216,218,220,221,224,237,240,253,255,256,281,294,296,299,300,310,314,322,326,329,331,335,337,348,355,361,363,365,370,375,395,396,399,402,424,434,458,459,469,470,472,474,475,476,478,479,481,484,486,487,488,490,499],evenli:[3,41,143,188,214,242,405,459],event:[],eventu:[3,6,12,15,170,290,483],ever:[54,56,238,314],evera:[385,398,434,450],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,115,121,130,156,171,191,192,193,194,195,197,198,199,200,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,225,228,229,231,233,235,236,237,242,243,251,255,256,260,279,280,281,285,286,287,288,289,290,291,292,294,296,297,299,300,302,303,314,316,317,318,319,320,321,322,325,326,327,328,329,337,339,354,356,365,366,367,370,391,392,402,415,432,433,440,446,463,464,465,469,471,473,474,476,477,478,483,484,485,487,495,499],everyth:[8,109],everywher:[118,409],eviri:395,evolut:[233,242,282,464],evolv:[242,282,327],ewald:[2,3,5,6,7,8,12,88,112,120,143,327,355,356,363,378,380,381,387,390,395,407,411,427,435,450,452],ewald_disp:390,ewalddisp:3,exact:[22,41,44,71,124,162,171,176,214,217,232,233,239,240,241,285,294,295,314,326,341,355,384,471,476,483,495,497,499],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,91,118,146,152,159,168,188,198,199,209,214,220,225,232,239,240,241,256,268,269,277,281,289,314,319,320,333,370,384,391,393,399,402,405,416,424,452,471,472,479,483,495],exager:490,examin:[6,8,9,17,217,281],examp:[467,495],exampl:[],exce:[3,6,16,17,18,41,58,71,170,205,206,209,210,211,212,214,218,220,225,228,255,281,296,300,305,306,314,363,370,469,495],exceed:[3,41,59,214,220,255,314,477],excel:395,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,110,111,114,119,143,145,146,147,148,149,150,151,152,154,155,156,157,158,159,160,161,168,172,174,175,176,177,178,179,180,182,183,185,186,187,188,190,191,194,197,200,206,207,209,213,214,218,220,227,230,231,234,237,239,241,255,256,257,258,259,260,261,262,263,264,265,268,269,272,274,275,276,277,278,282,291,292,299,301,302,311,314,317,319,320,326,330,334,337,339,340,341,342,343,345,346,349,350,351,355,356,358,360,364,365,366,368,369,370,371,372,374,378,379,380,381,382,383,384,385,386,387,389,390,391,393,394,395,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,417,420,425,426,427,429,432,433,434,435,442,450,451,452,453,454,455,457,458,460,461,462,464,466,467,469,471,472,474,477,478,479,480,481,483,487,490,494,495,496,498],excess:[208,395],exchang:[2,3,6,8,9,61,62,197,203,204,231,239,291,299,322,326,329,355,370,395,484],exchange:355,excit:[9,395],exclud:[3,6,9,12,16,17,63,71,114,142,148,155,156,172,191,206,210,215,216,243,251,284,297,299,321,332,337,363,364,366,379,399,402,416,417,424,449,481],exclus:[1,3,9,12,16,87,370,386,422,424,478,488],excurs:464,exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,169,193,236,293,339,354,357,369,465,467,477,480,483,495],exempl:440,exemplari:232,exemplifi:395,exert:[6,237,240,294,333,334,335,356],exhaust:[203,369,495],exhibit:[92,255,362,395,478],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,124,168,169,187,192,193,194,197,202,213,216,218,221,231,284,285,287,337,340,342,343,344,346,350,359,364,370,402,432,449,459,465,467,469,470,471,480,481,482,495,496,497],exit:[2,3,11,12,41,57,191,214,354,369,467,468,477,486,495],exlanatori:3,exp:[],expand:[],expans:[12,142,191,480,495],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,103,149,160,166,188,214,226,231,233,252,280,286,288,289,294,299,337,356,366,384,419,422,424,464,467,469,471,474,478,483,495],expens:[6,10,71,194,280,284,299,326,337,355,356,366,370,467],experi:[6,13,15,17,213,221,236,245,254,286,298,299,361,365,391,424,478,483],experienc:[6,12,244,245],experiment:[231,355,370,483],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,93,148,156,188,191,193,194,197,206,207,212,214,216,218,220,255,280,288,299,311,337,339,354,355,358,364,365,369,375,393,405,440,442,457,467,470,471,474,476,479,490,495,499],explan:[3,6,59,115,142,191,206,254,280,402,463,466,467,469,478],explanatori:[3,8,119,191,205,206,209,210,211,299,364,466,495],explantori:[3,295],explic:423,explicit:[6,9,11,22,44,77,87,115,118,162,176,198,199,220,305,306,341,360,372,373,377,382,384,393,395,406,416,456,463,466,470,473],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,111,114,145,155,158,166,168,174,175,177,178,179,180,182,183,185,186,188,191,194,200,210,213,220,227,230,232,234,239,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,288,289,291,299,301,302,317,319,320,326,330,334,340,342,343,345,346,349,351,364,370,371,372,374,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,396,397,398,399,400,401,402,405,406,407,408,409,410,411,412,413,414,415,416,420,422,424,425,426,427,429,434,435,442,443,444,445,446,447,448,450,451,452,453,454,455,456,457,458,460,461,462,469,471,472,478,479,481,482,488,490],explictli:[16,482],exploit:[9,15,17,282],explor:[120,167],expon:[3,290,292,393,398,401,415,423,435],exponenti:[87,430,451,458,462,483,495],expos:11,exposit:[203,391,392],express:[6,142,154,168,198,199,218,252,280,290,326,332,339,377,393,395,409,419,440,441,450,495],expressiont:377,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,95,98,99,109,111,119,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,197,200,201,204,212,213,219,222,226,229,230,231,233,234,235,237,239,241,253,255,260,269,280,281,297,298,299,301,303,308,311,313,317,318,319,320,321,323,324,326,328,331,335,336,398,419,422,433,434,441,486,487],extent:[1,3,41,42,45,57,71,166,170,191,202,210,214,237,333,336,355,358,372,436,438,452,466,469,472],exterior:[3,6,335],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,103,111,112,114,120,143,145,146,147,149,151,154,155,156,157,158,160,161,167,168,169,170,174,194,209,214,216,255,287,288,289,299,314,363,364,367,368,390,399,402,405,419,424,466,467,469,472,481,490,495],extract:[3,6,11,13,36,63,87,109,117,119,121,198,199,292,365,387,396,419,441,467,474,486],extract_atom:11,extract_comput:[11,467],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,193,208,218,220,255,324,395,454,490],extrema:415,extrins:203,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[164,328],f_a:[453,454,455],f_ave:119,f_c:454,f_f:455,f_fix_id:289,f_harm:324,f_i:[29,430],f_id:[6,71,119,121,191,197,205,206,207,208,209,210,211,212,250,316,328,487,495],f_ij:430,f_indent:212,f_int:323,f_j:29,f_jj:91,f_k:430,f_langevin:326,f_max:[289,294],f_msst:253,f_r:[240,453,454,455],f_sigma:377,f_solid:324,f_ss:6,f_temp:[],face:[3,6,57,59,71,156,166,170,202,210,211,331,333,334,335,336,358,398,419,434,469,472],face_threshold:166,facet:166,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,233,314,324,399,440,481],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,87,91,103,110,117,118,120,142,162,167,170,174,185,190,191,193,194,198,199,207,214,218,220,221,231,236,239,241,242,253,255,256,260,282,286,298,302,304,306,314,318,322,329,330,331,335,346,356,358,364,370,372,373,377,378,380,382,387,388,389,391,395,399,402,406,407,419,422,424,426,427,433,435,442,451,456,466,469,472,473,478,481,483,484,487,490,494,495],factori:[3,467],factoriz:355,fail:[3,11,12,59,172,218,221,355,363,365,389,433,467],failur:[123,437,468,495],fairli:[11,424,478,483],faken:73,falcon:236,fall:[3,6,194,209,285,467,495],fals:[86,337,339,440,495],fame:8,famili:[458,466],familiar:[0,11],fan:430,far:[3,6,12,17,57,59,61,86,191,194,195,214,215,216,218,221,255,280,298,299,314,331,342,346,361,365,366,457,467,469,474,487],farago:239,farrel:[453,455],farther:191,fashion:[6,8,41,71,168,194,197,198,199,204,210,214,216,221,231,233,237,252,253,255,257,258,259,260,261,262,263,271,274,275,276,277,278,288,289,291,299,303,307,313,316,324,326,330,331,332,334,336,365,402,416,472,481,495,498],fasolino:404,fast:[6,7,9,12,13,17,39,191,266,289,327,355,356,379,416,417,422,450,452,471,476,478,487,496,499],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,106,111,114,145,155,174,175,177,178,179,180,182,183,185,186,188,191,194,200,213,214,220,227,230,234,238,239,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,286,290,291,299,301,302,314,317,319,321,323,326,330,334,340,342,343,345,346,349,351,355,356,367,368,370,371,372,374,377,378,379,380,381,382,383,384,385,386,387,390,391,393,394,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,420,425,426,427,429,434,435,442,450,451,452,453,454,455,457,458,460,461,462,464,472,478,482,490],fastest:[1,6,14,17,156,210,326,327,370,466],fatal:[3,486],fault:[70,433],faulti:12,fava:398,favor:217,favorit:7,fbmc:321,fcc:[],fcm:[271,495],fdirect:224,fdotr:403,fdti:87,fe2:167,fe3:167,fe_md_boundari:203,featu:8,featur:[],fecr:393,feedback:[7,236],feel:[7,236,237,245,280,335,337,365,424],felling:421,felt:335,femtosecond:494,fene:[],fennel:[387,407],fep:[],ferguson:[6,174,481],fermi:[1,12,15,154,370,455],fermion:[9,395],fernando:418,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,195,205,206,207,209,210,211,212,240,255,285,288,290,302,328,355,363,364,365,372,440,466,469,474,478,480,488,495,497],fewer:[1,3,11,15,16,61,245,478],fewest:3,fextern:229,feynman:282,fff:467,ffield:[386,396,432,433,440],ffmpeg:[3,12,193],ffplai:193,fft:[1,3,7,12,14,15,88,111,112,143,281,355,356,478],fft_inc:[12,356],fft_lib:12,fft_path:12,fftbench:[355,488],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:449,fictiti:[6,200,201,226,229,233,282,298,387,407,411,449],field1:[470,474],field2:470,field:[],fifth:[311,426],figur:[1,3,8,11,12,289,466,467],fij:390,file0:280,file1:[11,13,280,325,339,364,474,476,480],file2:[11,13,325,339,364,474,476,480],file:[],file_from:192,filen:364,filenam:[3,12,13,38,41,56,188,191,193,194,195,203,206,207,208,209,210,211,212,214,219,280,284,287,290,291,292,295,296,299,300,325,326,352,353,354,364,365,371,372,377,387,393,394,396,404,419,420,421,426,430,431,432,433,440,441,451,452,453,454,455,458,465,466,467,470,471,476,480,487,495,497,498,499],filennam:476,filep:[3,191,194,471,476,499],filepo:296,fill:[7,9,168,193,285,326,358,366,377,422,433,472],filter:[194,203],final_integr:8,final_integrate_respa:8,finchham:[6,150,389],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,119,171,188,195,204,217,218,228,231,254,280,286,294,298,361,363,365,366,387,402,407,411,419,440,450,452,490,495],find_custom:8,fine:[16,17,172,200,226,324,366,370,495],finer:[142,168,495],finest:355,finger:[168,190,252,472],finish:[6,11,41,214,339,352,354,355,367,369,370,457,474,495,496],finit:[],finni:[7,393,450],finvers:224,fiorin:[9,219],fire:[361,362,363,365,483],firebrick:194,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,104,105,106,108,114,118,119,129,132,135,136,140,143,153,156,162,164,166,167,169,170,171,175,188,191,192,193,194,195,197,198,206,207,209,210,211,212,214,217,220,231,232,237,242,252,253,254,255,280,282,287,288,289,291,296,299,302,303,311,312,314,315,316,323,324,325,326,328,332,337,339,340,347,358,363,364,365,366,369,370,371,372,375,377,378,380,382,384,386,387,393,395,396,399,400,402,403,404,406,407,411,416,417,419,421,422,424,426,430,432,433,440,441,449,451,452,453,454,455,458,462,464,465,466,467,469,470,471,474,476,478,481,482,483,486,487,490,495,496,497,499],fischer:[6,9,19,20,174,382,481],fit:[3,6,9,12,38,56,188,298,314,372,377,404,419,424,445,452,454,477,495],five:[73,154,289,364,377,420,469,483],fix:[],fix_adapt:[162,199,415],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,204,285],fix_evapor:204,fix_flux:203,fix_gcmc:[204,364],fix_gl:233,fix_gld:233,fix_grav:285,fix_id:[3,218,253,255,257,258,259,260,261,262,263,286,289],fix_modifi:[],fix_mov:[190,332],fix_nh:8,fix_npt:233,fix_nvt:[204,231],fix_poem:[3,6],fix_pour:[3,221],fix_qbmsst:9,fix_qeq:[3,386],fix_rattl:302,fix_reax_bond:432,fix_rigid:[245,375],fix_saed_vtk:300,fix_setforc:8,fix_shak:302,fix_srd:3,fix_styl:260,fix_temp_rescal:320,fixedpoint:[218,255],fixextern:229,fixid:203,fji:390,flag1:[223,368],flag2:[223,368],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,94,104,105,107,120,163,167,171,191,193,194,195,212,217,219,223,236,239,243,245,251,252,281,288,299,311,313,314,321,325,334,337,353,356,364,368,369,370,372,401,406,419,422,449,464,466,467,469,470,471,473,474,475,479,495],flag_buck:381,flag_coul:[381,390,411],flag_lj:[390,411],flagfld:[379,416,417],flaghi:[3,379,416,417],flaglog:[379,416,417],flagn:223,flagvf:[379,416,417],flat:[6,326,331,332,336],flavor:[2,7,12],fld:[9,331,379,416,417],flen:373,flex_press:373,flexibl:[3,6,8,169,193,206,210,219,233,256,322,329,395,454,487],flip:[3,6,220,255,333,334],floor:495,flop:12,floralwhit:194,flow:[],fluctuat:[6,64,87,218,231,232,239,242,255,260,280,281,324,326,349],fluid:[],fluid_veloc:246,flush:[3,194,486],flux:[],flv:193,fly:[7,9,12,41,193,197,203,208,221,224,299,302,327,377,422,487,490],fmackai:9,fmag:222,fmass:282,fmax:[363,487],fmomentum:224,fmsec:[2,194,239,240,252,255,286,299,317,318,478,489,494,496],fname:354,fno:[12,16],fnorm:[363,487],fnpt:224,fnvt:224,foce:402,fock:373,focu:302,fogarti:[9,292,433],foil:[142,280,441],fold:[312,478],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,92,97,98,108,115,118,119,121,142,143,146,147,148,154,156,161,164,166,168,169,174,177,178,179,180,182,183,185,186,188,191,192,193,194,197,203,204,205,206,207,208,209,210,211,212,214,219,220,221,224,225,229,231,232,233,236,238,239,240,242,245,253,255,260,261,262,263,274,275,276,278,281,282,284,287,288,289,290,292,294,296,298,299,300,302,316,317,318,319,322,323,324,325,326,328,329,337,338,342,343,344,345,346,349,351,353,358,360,363,364,365,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,429,430,431,432,433,434,435,437,439,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,456,457,458,460,461,462,464,466,467,469,470,472,474,476,477,478,481,483,484,485,490,495,496,498],foo:[4,8,11,12,191,193,229,467,480,495],foot:6,footprint:[12,370],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:245,forcefield:[298,401],forcegroup:242,forcezero:361,ford:390,forestgreen:194,forev:71,forget:[240,490],forgiv:255,fork:[12,191],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,87,89,90,92,94,104,105,107,118,142,143,162,163,172,176,194,197,198,199,216,232,233,239,241,245,252,276,281,292,294,298,299,326,331,335,340,341,344,349,360,362,364,365,372,373,377,384,393,395,397,401,402,406,418,419,421,422,426,427,430,432,433,434,440,441,442,450,452,453,454,455,461,463,466,467,469,474,479,486,490,495],formal:[6,78,80,91,232,233,239,255,282,314,322,440],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,176,188,191,192,193,194,195,206,209,210,211,212,214,216,281,284,288,290,292,295,299,300,310,325,326,337,338,341,360,364,365,371,372,377,384,393,396,406,419,421,431,432,433,435,441,452,458,459,466,467,469,470,471,474,485,486,487,495,497],former:[6,12,16,39,41,194,214,326,330,377,379,475,481,495],formerli:[7,13],formul:[1,40,64,143,200,226,239,255,276,290,292,298,302,325,355,372,377,393,395,398,419,429],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,95,97,98,107,114,120,143,145,146,147,148,149,150,151,152,154,155,156,157,158,159,160,161,167,168,173,175,176,187,190,191,198,199,200,201,206,207,208,209,212,213,220,226,234,235,237,239,240,252,280,281,287,296,301,308,312,314,317,318,319,328,331,334,336,337,339,340,341,343,350,358,364,372,373,375,377,382,383,384,385,390,391,393,394,398,399,400,401,403,406,407,409,410,411,413,414,416,417,419,423,424,425,434,435,442,450,451,453,454,455,458,460,461,465,469,472,479,486,487,494,495,496],forth:[1,6,11,12,13,14,15,369,467,472,476],fortran:[3,6,9,11,12,13,229,393,402,419,432,433],fortun:8,forward:[3,8,87,354,365,370],foster:[377,429,430],foul:171,found:[3,6,9,12,73,162,191,217,219,231,236,242,281,321,327,339,354,366,384,387,390,464,470,471,486],four:[6,11,54,81,104,105,142,164,253,326,349,364,365,422,464],fourier:[],fourth:[6,106,298,311,321,382,426,440],fox:[6,120,174,448,481],fphi:[38,56,452],fpic:12,fplo:[38,56,452],fprime:452,fqdn:238,fqq:390,frac:[],fraction:[1,3,6,8,12,16,39,41,80,111,143,171,190,193,194,204,215,216,217,218,253,285,289,296,297,314,319,320,358,365,370,377,379,399,416,417,474,479],fragment:[42,236,296],fraig:[42,376],frame:[83,142,194,203,253,289,333,398],framer:[193,194],framework:[5,233,371,441],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,87,162,199,280,314,323,324,325,326,362,365,373,395,415,422,430,461,466],freedom:[3,6,8,95,97,98,100,102,103,114,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,161,206,217,224,231,233,239,240,245,255,256,260,261,262,263,274,275,276,278,282,284,299,302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39,441,458],input1:[65,68,69,79,93,110,115,116,117,119,121,316],input2:[65,68,69,79,93,110,115,116,117,119,121,316],input:[],input_doubl:3,inquir:304,insensit:12,insert:[3,5,7,8,12,59,168,197,221,231,237,285,355,441,449,467,473,490],insid:[2,3,6,8,11,71,131,137,168,191,194,205,210,211,221,222,228,231,237,242,245,285,299,314,331,333,334,335,336,337,353,358,409,467,468,469,471,472,479,483,495],insight:[6,13],instabl:[242,390,439],instal:[],instanc:[6,11,198,219,233,333,397,402,424,430,467,490],instantan:[6,63,217,218,232,233,255,260,281,286,289,294,296,299,321,475,487],instanti:[6,11,12,203,402,466],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,61,63,70,71,90,104,119,146,150,172,188,191,199,206,209,210,211,212,214,218,219,231,239,242,245,246,281,287,297,299,316,334,353,355,356,359,366,370,380,381,393,406,408,415,419,422,464,472,476,483,485,490,495],institut:[9,236,284],instruct:[],insuffici:[3,6,12],insult:255,insur:[3,6,11,12,17,39,40,61,73,103,105,168,169,188,191,193,194,200,215,216,221,226,227,228,229,231,234,239,251,287,288,297,299,314,326,331,335,336,337,339,354,364,366,370,385,398,402,428,434,452,466,467,469,470,474,477,478,486,487,495,496],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,108,115,117,119,121,142,166,168,171,172,174,178,179,183,188,190,191,193,194,204,206,210,211,215,216,217,221,223,229,231,232,233,236,239,240,241,242,281,284,285,288,289,294,299,314,316,318,321,325,326,345,355,358,379,391,392,405,419,432,433,437,439,441,464,466,467,468,469,477,478,479,483,486,495,496],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,208,232,431,469],intens:[1,3,6,9,63,66,74,75,86,89,90,91,94,104,105,106,107,114,116,118,119,120,121,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,163,164,165,167,197,206,207,209,210,211,212,214,215,216,217,225,228,235,245,253,255,260,296,299,300,314,322,326,328,329,486,487],intepol:495,inter:[14,18,42,61,62,148,171,172,191,217,239,241,254,291,299,355,365,377,479,490,495,497,499],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,42,44,50,54,55,57,61,63,65,69,72,77,79,87,88,92,93,108,109,110,112,114,117,118,124,125,126,127,129,130,131,132,133,134,135,137,138,139,140,142,143,144,146,147,161,162,166,169,170,171,172,173,174,176,180,181,187,191,197,198,199,215,216,217,230,231,236,237,239,241,245,269,280,282,284,290,292,298,299,305,306,314,315,321,326,330,331,332,335,336,341,342,343,344,346,350,355,356,363,364,365,366,367,368,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,429,430,433,434,435,437,439,440,441,442,449,450,451,453,454,455,456,457,458,459,460,461,462,464,467,469,471,473,474,478,479,481,486,487,490,497],interatom:[3,4,7,168,191,254,323,324,371,377,393,395,403,419,422,440,454,495],intercept:120,interchang:6,interconnect:18,interconvert:395,intereract:39,interesect:335,interest:[1,5,7,8,9,11,13,71,167,282,321,324,356,394,417,432,433,467,495],interf:370,interfac:[],interfer:[12,255,372],interg:[6,490],intergr:[478,482],interi:417,interior:[3,6,41,335,472],interlac:419,interleav:[6,168,477],intermedi:[6,12,59,193,254,280,349,365,467,468,477,481],intermix:464,intermolecular:372,intern:[0,2,3,5,6,9,11,16,20,21,24,28,32,35,36,39,40,42,63,87,100,102,120,143,148,150,167,175,188,193,194,197,198,199,203,216,220,224,236,248,249,253,255,260,281,299,303,340,342,346,349,353,363,364,443,444,452,467,469,471,474,483,486,487,494,495,496,497],internal_element_set:203,internal_quadratur:203,internet:238,interpenetr:419,interpentr:[444,445,447],interpol:[6,15,38,56,101,188,193,194,203,242,280,355,356,365,377,424,433,446,452,453],interpret:[2,6,11,193,209,399,442,464,467,483,495],interrupt:289,intersect:[3,6,120,194,335,337,472],intersert:335,interspers:363,interstiti:[166,422],intertia:[3,94],interv:[3,6,91,192,207,239,289,294,295,306,440,446,464,483,495],intestieti:120,intial:[6,370,372],intiial:[41,474],intiti:[3,313],intra:299,intra_energi:231,intramolecular:[29,231],introduc:[6,9,92,108,193,255,289,294,299,349,355,371,387,395,407,411,415,451,483,495],introduct:[],intsal:[],intuit:358,inv:[120,167,300],invalid:[3,12,71,89,171,269,365,416,417,471],invari:[108,135,140,142],invent:302,invers:[],invert:[1,6,172,281],invis:335,invoc:[166,217,370,437,439,467],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,87,88,89,90,94,104,105,107,111,112,113,114,119,145,155,162,163,166,168,169,171,172,174,175,177,178,179,180,182,183,185,186,188,191,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,225,226,227,228,229,230,231,232,234,235,236,237,239,240,241,242,243,244,245,246,247,248,249,251,252,254,255,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style body/rounded/polygon command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":215,"default":[37,39,40,55,57,58,59,61,62,71,87,88,92,103,104,106,108,109,120,124,125,142,148,156,157,161,167,168,171,173,187,189,190,191,193,194,195,196,198,199,200,202,203,204,206,210,211,212,215,216,218,219,220,221,225,228,231,232,237,239,240,241,242,243,245,250,253,255,256,260,276,277,281,282,285,286,287,288,289,291,294,296,297,299,300,314,316,321,322,323,324,327,329,331,333,337,350,353,355,356,358,359,361,362,364,366,367,368,370,373,377,379,395,416,417,422,424,432,433,449,450,464,465,466,469,470,472,474,476,477,478,481,483,485,486,487,488,489,494,496,497,498],"function":495,"long":[208,378,380,381,382,383,387,389,390,407,411,415,427,435],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[198,199],addforc:200,addit:[12,13],addtorqu:201,adiabat:6,adjust_dt:304,adp:371,airebo:372,alloi:393,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:202,arrai:6,aspher:[6,82,146,257,261,265,266,274],atc:[9,203],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,92,96,97,100,101,102,108,112,113,115,142,143,166,202,204,205,288,495],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:213,awpmd:[9,373],balanc:[41,214],barostat:6,basal:67,beck:374,berendsen:[286,317],between:6,binary2txt:13,bodi:[6,8,42,68,147,258,262,267,275,375,376],bond:[8,13,69,215,216,217,295],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:377,born:[378,389],boundari:[7,57],box:[6,58,218],brownian:379,buck:[380,381,389,418],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,174,382,415],chunk:[6,66,71,75,90,94,105,107,116,148,163,165,206],citat:7,class2:[21,43,175,340,383],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[331,385,461],colvar:[9,13,219],com:[74,75,149],comb3:386,comb:[291,386],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,495],compute_modifi:103,condit:7,conduct:[6,322],constant:6,constraint:7,contact:76,contact_radiu:122,coord:77,core:6,correl:[207,208],cosin:[23,24,25,26,27,28,177],cossq:342,coul:[378,380,381,382,383,387,388,389,400,407,411,415,427,435],coupl:6,creat:216,create_atom:168,create_bond:169,create_box:170,createatom:13,creation:7,csld:318,csvr:318,cubic:409,cuda:[9,14,111,114,145,155,200,213,227,230,234,255,264,301,302,317,319,330,378,380,382,383,393,399,400,407,408,410,413,425,451,453],custom:8,cut:[49,373,380,383,387,390,395,397,407,408,415,423,427],cvff:343,damag:[78,123],data2xmovi:13,data:6,databas:13,deby:[387,407],dec:0,deform:[151,152,220],delete_atom:171,delete_bond:172,delta:24,deposit:221,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],diagnost:7,diel:388,dielectr:173,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:176,dihedral_styl:[2,174,175,177,178,179,180,181,182,183,184,185,186,187,188],dilat:80,dimens:189,dipol:[6,29,390],direct:224,discuss:6,disp:6,displac:[81,86],displace_atom:190,distanc:344,distribut:[7,12],document:0,dpd:391,drag:222,dreid:[6,401],drude:[6,9,153,223,224,240],dsf:[387,407],dsmc:392,dump:[6,8,191,192,193,195],dump_modifi:194,dynam:290,eam:[13,393],echo:196,edip:394,eff:[9,13,97,98,152,154,159,241,256,268,277,320,395],efield:226,eim:396,elast:6,emac:13,enforce2d:227,ensembl:7,erot:[82,83,84,85],error:3,evapor:228,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],exp:[27,177],expand:[46,410],extend:[8,11],extern:229,fcc:280,featur:[7,8,495],fene:[45,46],fep:[9,13,87,199],field:[6,7],file:6,finit:6,fix:[2,6,8,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,495],fix_modifi:[198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,21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air_coeff:384,pair_modifi:424,pair_styl:[2,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,460,461,462],pair_writ:459,pairwis:8,parallel:11,paramet:6,pars:2,partial:155,particl:[6,7,42],partit:463,past:5,per:6,perform:[1,10],peri:429,period:25,phonon:[9,13,281],pimd:282,piston:333,planeforc:283,plastic:113,plastic_strain:126,plastic_strain_r:127,pmb:429,poem:[9,284],point:290,polariz:6,poli:[379,416,417],polygon:376,polym:13,polymorph:430,post:7,potenti:[2,6,8],pour:285,pppm:6,prd:464,pre:7,press:286,pressur:114,previou:12,print:[287,465],problem:[3,4],process:[6,7],processor:466,profil:156,properti:[6,115,116,117,288],pymol_aspher:13,python:[9,11,13,467],qbmsst:289,qeq:[290,291,292],qmmm:[9,293],qtb:[9,294],quadrat:186,quantiti:6,quartic:[35,54],quip:431,quit:468,ramp:157,rattl:302,rdf:118,read_data:469,read_dump:470,read_restart:471,reax:[9,13,292,295,296,432,433],reaxc:9,rebo:372,recent:297,reduc:119,refer:495,reflect:334,region:[8,119,158,159,335,472,495],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,97,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,185,186,187,188,189,190,191,192,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,228,230,231,232,233,234,235,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,294,295,296,297,299,300,301,303,304,305,306,307,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,349,350,351,352,353,354,355,356,358,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,474,475,476,477,478,479,481,482,483,484,485,486,487,488,489,491,492,493,495,496,497,498,499],relax:218,replic:473,replica:[6,7],report:3,requir:12,rerun:474,rescal:[319,320],reset:225,reset_timestep:475,resquar:434,restart2data:13,restart:[6,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,476],restrain:298,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],rho:128,rhosum:446,rigid:[6,83,99,245,299],ring:349,rotat:160,round:376,rule:2,run:[6,11,12,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,477],run_styl:478,scalabl:10,scalar:6,screen:12,script:[2,6,8,11],sdk:[36,435],self:313,serial:11,set:[6,479],setforc:301,setvel:308,shake:302,share:[11,12],shell:[6,480],shield:290,shift:[26,27,48,49,177],simpl:31,simul:6,size:6,slater:290,slice:121,sllod:[276,277],small:299,smd:[9,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,303,304,305,306,307,308,310,436,437,438,439],smooth:[413,414],smtbq:[9,440],sna:142,snad:142,snap:441,snapshot:6,snav:142,soft:[415,442],solver:2,sourc:7,spatial:[210,211],spc:6,speci:296,special:[7,424,495],special_bond:481,sph:[9,443,444,445,446,447,448],sphere:[84,85,161,211,245,259,263,272,278],spheric:6,spline:[420,421],spring:[311,312,313,324],squar:28,srd:[314,336],srp:449,standard:9,start:[12,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336],state:316,stationari:249,stop:[198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336],store:[315,316],strategi:1,streitz:387,stress:[143,144],structur:2,style:[1,2,6,8],submit:8,suffix:482,summari:6,swap:[204,217],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,281,282,283,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],system:6,tabl:[0,6,38,56,188,452,453],tad:483,ta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\ No newline at end of file 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,chip:[7,12,17,18,370,482],chipot:219,chiral:349,chmod:[11,12],cho:419,chocol:[7,194],choic:[3,6,12,15,16,18,40,41,54,87,143,146,147,161,172,188,206,210,211,214,217,220,221,233,239,242,253,255,282,290,299,321,350,356,361,362,365,367,370,402,415,424,428,469,478,479,482,483,489,490,494],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,119,158,159,193,215,216,217,218,221,228,239,242,253,255,257,258,259,260,261,262,263,286,314,318,332,355,356,362,459,464,466,478,484],chose:[453,455],chosen:[2,3,6,12,17,142,168,171,180,188,193,199,204,218,221,228,231,232,240,242,253,255,260,282,285,296,314,318,321,322,327,329,330,336,356,357,362,370,395,399,405,406,409,435,453,464,478,483,490],chri:166,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,94,105,107,116,148,163,165,206],chute:[4,10,234],ciccotti:302,cieplak:[6,174,481],cii:207,cij:207,circl:[42,71,310],circular:[3,6,146,189],circumst:18,circumv:[92,108,294],citat:[],cite:[3,7,8,12,239,440],ckio:2,cko:2,cl1:167,clarendon:[29,390],clarifi:[7,453,455],clariti:339,clark:427,class2:[],classic:[0,3,5,6,7,8,9,229,282,289,294,326,351,395],classifi:[9,450,458],claus:467,clean:[6,12,14,15,17,477],cleanli:[468,498],clear:[],clearli:7,clebsch:142,clermont:[9,13],clever:473,click:[2,11,22,37,44,55,168,176,187,193,236,341,350,365,384,450],client:[236,238],climb:[254,365,483],clinic:[7,13],clo:[157,190,496],clock:[12,464,483],clockwis:332,close:[3,6,11,12,13,39,41,67,143,171,191,216,217,218,233,240,242,255,276,299,302,332,335,354,356,359,361,362,365,370,372,377,387,388,419,424,436,438,455,473,479,490,492],closer:[3,41,118,166,190,191,214,218,222,323,365],closest:[216,280,299,329,398,434,449,459],cloud:[440,490],clovertown:18,clsuter:72,clump1:[284,299],clump2:[284,299],clump3:[284,299],clump:299,cluster:[],clutter:[3,9],cmap:469,cmatrix:233,cmax:419,cmd:[11,12,282,480],cmdarg:11,cmin:419,cmm:[],cn1:207,cn2:207,cna:[],cnn:207,cnr:[9,13],cnt:[402,473],co2:[40,167,302,364],coars:[7,9,29,36,40,54,180,284,299,314,400,435,481],coarser:[356,495],coarsest:142,code:[],coeff:[3,7,8,12,21,22,33,44,50,174,175,176,181,340,341,347,384,402,406,424,437,439,442,469],coeffcient:469,coeffici:[],coefficienct:391,coefficient0:393,coefficient1:393,coeffieci:[6,374],coeffincientn:393,coexist:[9,231,395],cohes:[6,396,419],coincid:[124,335,382,416,417,464],colberg:192,cold:[6,153,231,235,366,490],coldest:322,coleman8:9,coleman:[9,120,167,300],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,94,99,105,107,116,148,156,163,165,168,191,194,206,219,245,251,284,294,297,299,337,355,364,366,385,405,469,476,482,488,499],collid:[225,314,336],colliex:167,collinear:[3,284],collis:[3,242,314,332,336,392,399,462],colllis:314,colloid:[],colombo:39,colon:[195,337,470],color1:194,color2:194,color:[3,9,41,191,193,194,214,232,289,294],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,94,105,107,108,110,112,115,116,117,118,119,121,142,143,148,156,163,165,166,167,188,191,194,197,205,206,207,209,210,211,212,245,252,253,289,299,315,316,326,336,397,401,432,433,470,484,486,495],colvar:[],colvarmodul:12,com:[],comamnd:220,comand:217,comannd:370,comb3:[],comb:[],comb_1:291,comb_2:291,combiant:388,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,93,104,110,117,146,147,161,191,193,203,209,236,245,255,282,288,318,327,335,338,340,355,356,358,362,370,385,387,388,395,396,402,414,415,441,451,453,455,458,461,472,477,482,490,495],come:[],comfort:[12,13],comm:[0,3,11,12,61,73,192,236,238,239,356,365,370,391,424,429,452,471],comm_modifi:[],comm_modift:61,comm_styl:[],comm_world:11,command:[],comment:[2,7,11,12,38,56,174,188,191,240,299,326,364,365,371,393,394,396,406,419,426,433,440,441,451,452,453,454,455,458,466,467,469,490,495],commerci:7,commmand:[3,6,12,59,109,277,463,464,466,483,498],common:[],commonli:[3,6,12,17,25,57,59,106,108,170,191,193,195,351,400,409,441,453,455,469,472,481],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,171,172,193,194,214,215,216,218,219,220,236,238,242,244,245,246,255,281,288,290,291,292,299,314,326,337,353,355,366,367,368,370,392,428,466,467,478,479,495,497,499],communc:355,comp:[7,192,238,239,302,356,365,395,424,429,434,448,452,454],compact:[63,197,384,450],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,112,120,151,166,167,176,187,194,224,290,337,339,355,356,363,365,419,440,464,483,484,490,494],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,175,176,187,340,341,350,383,450],compat:[3,5,7,8,9,11,12,13,17,18,41,71,119,121,179,191,195,199,205,206,207,209,210,211,212,214,281,293,318,321,328,331,334,355,370,403,422,424,452,466,467,495],compens:[6,215,216,297,366,395],compet:325,competit:356,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,166,191,192,193,195,236,325,356,370,422,469,470,474,495],compl:17,complain:[12,17],complement:419,complementari:[7,387,407],complet:[3,6,9,11,12,15,41,59,71,194,210,214,219,245,282,285,288,314,325,327,339,354,365,370,396,437,439,457,464,469,474,477,481,483,486,490,495],complex:[6,8,11,12,13,25,40,42,62,92,108,142,144,156,168,169,242,310,335,353,365,395,422,452,467,469,472,495],compli:[321,325],complic:[6,7,9,12,13,204,231,467],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,92,94,95,98,105,106,107,108,109,110,111,112,114,115,119,129,132,133,134,135,138,139,140,142,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,161,163,164,165,190,191,193,194,200,201,205,206,207,208,209,210,211,212,213,217,218,220,221,226,229,234,238,239,242,245,247,251,252,254,255,256,260,261,262,263,274,275,276,278,279,281,282,283,286,297,299,301,302,303,307,308,311,314,317,318,319,321,328,329,334,335,336,355,358,362,363,364,365,370,376,391,395,399,416,417,437,439,440,441,469,470,479,487,495,496],componenet:6,composit:[6,204,242,393],compound:[386,395,396,458],compres:[71,116,206],compress:[],compris:[40,335,405,434,457],compton:[120,167],comptu:3,compuat:356,comput:[],computation:[3,6,215,216,326,377],computational:490,compute_arrai:8,compute_fep:[199,415],compute_group_group:231,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[120,300],compute_scalar:8,compute_temp:8,compute_ti:199,compute_vector:8,compute_xrd:167,concaten:[2,3,498],concav:335,concentr:[71,393],concept:[6,148,158,206,478],conceptu:[3,6,71,156,218,220,365,387,402,419,474],concern:[6,73,87,192,232],concetr:71,concis:[11,325],conclud:12,concret:8,concurr:[9,16,356,495],conden:[326,453,455],condens:[6,150,326,372,389,393,407,458],condit:[],conducit:6,conduct:[],cone:472,confer:422,confid:[3,483],config:[12,191,466],configfil:219,configur:[1,2,6,12,15,17,38,59,124,170,188,190,191,193,197,218,219,220,221,225,231,238,239,269,282,290,325,353,363,365,372,377,394,419,422,451,453,455,458,464,469,471,472,483],confin:[469,483],conflict:[3,12,40,424,467],conform:[3,6,13,59,217,218,254,298,303,325,349,365,395,481],confus:[3,458],conjuct:391,conjug:[7,8,239,362,395,432,433],conjunct:[6,7,71,86,87,116,151,156,162,168,172,194,198,199,239,242,246,269,285,286,290,291,292,294,299,314,322,329,334,355,356,365,378,380,384,387,391,395,401,407,424,427,435,456,469,472,476,490,499],connect:[3,6,87,153,171,217,236,284,299,302,311,365,388,399,449,455,466,467,473,490],conput:3,consecut:[3,11,12,39,71,168,194,198,199,221,236,237,387,407,411,464,470,472],consequ:[1,6,204,326,406,483],conserv:[3,29,197,204,217,224,225,232,235,239,241,242,246,251,253,255,269,299,302,317,318,322,329,330,334,365,390,391,399,413,440,478,483],consid:[6,9,70,71,78,87,117,150,153,154,171,191,194,198,199,205,207,210,214,216,217,221,243,256,281,299,321,322,325,326,329,356,384,395,402,433,434,440,449,464,465,467,470,471,472,474,477,479,487,490,495],consider:[6,8,239,240,317,318,319,370,478],consist:[3,6,8,9,11,12,40,42,65,69,79,93,105,110,113,114,117,148,151,153,168,180,190,195,200,201,206,220,221,224,226,229,232,239,240,241,252,255,257,258,259,260,261,262,263,264,265,267,268,269,270,272,273,274,275,276,277,278,286,289,294,296,298,299,317,318,319,320,330,355,356,358,364,365,370,372,377,379,385,387,395,398,402,416,417,419,422,424,434,437,439,440,452,459,467,469,470,471,472,473,474,481,490,495],consistent_fe_initi:203,consit:299,constant:[],constitu:[3,6,245,299,331,335,385,434],constitut:[437,439],constrain:[3,6,8,145,146,147,148,149,151,154,155,156,157,158,160,161,197,206,221,231,232,237,245,249,284,285,297,299,302,312,322,329,363,364,395,474,481,490],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,92,108,120,142,167,218,255,281,298,335,366,370,390,422,424,449,451,452,472,473,488,495],constructor:[8,11],consult:433,consum:[1,294,428,495],consumpt:353,contact:[],contact_stiff:[436,438],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,118,120,142,148,156,166,167,168,170,174,176,187,188,191,193,194,195,197,198,199,203,205,206,207,209,210,211,212,214,219,221,226,233,237,238,239,242,253,269,280,281,284,285,287,289,292,296,299,300,304,314,321,325,326,335,336,339,354,356,364,365,368,369,371,372,373,377,386,387,390,393,394,395,402,403,419,422,426,430,431,432,433,441,451,452,453,454,455,456,458,464,465,466,467,469,470,471,472,474,476,478,481,483,486,487,490,495,497,499],content:[12,18,433,485,487],context:[3,6,8,12,17,118,119,194,215,216,221,284,296,330,362,461,469,476,485,494,495,496],contibut:70,contigu:466,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,104,105,164,194,197,198,199,204,206,207,208,209,210,211,212,214,217,218,219,220,221,231,232,233,235,236,237,239,240,241,247,252,253,255,257,258,259,260,261,262,263,274,275,276,277,278,283,285,288,289,299,300,303,313,314,316,323,324,326,332,335,339,354,369,370,377,391,392,409,412,432,433,434,437,439,454,464,467,469,471,472,477,483,486,487,495,497],continuum:[6,7,9,203,326,437,439],contour_integr:203,contract:[59,218,220,255,286,299],contradictori:3,contrain:302,contraint:269,contrari:[233,240],contrast:[1,6,42,55,64,150,153,220,337,437,439,461,498],contrib:326,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,94,103,105,107,109,110,111,112,114,116,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,199,204,205,206,207,209,210,211,212,218,231,239,242,245,246,250,256,276,277,284,285,293,296,299,300,302,328,355,363,365,373,391,392,393,395,402,416,417,422,424,432,433,440,481,487,490],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,124,142,177,191,193,197,203,204,214,218,219,220,235,236,239,240,255,257,258,259,260,261,262,263,286,291,299,305,306,317,318,319,326,330,353,355,367,395,398,422,432,433,436,438,451,455,464,466,478,484,485],control_typ:203,controlfil:433,convect:91,conveni:[6,12,29,191,195,212,300,358,441,495],convent:[3,8,9,29,179,186,187,194,298,311,338,393,395,495],converg:[3,6,41,88,191,193,195,200,214,217,218,226,229,260,289,291,294,298,302,361,362,363,365,386,387,407,440,464,476,483],convers:[3,8,142,193,194,204,207,286,355,387,388,389,395,407,411,415,427,467,483,494],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,168,175,191,193,194,212,253,337,340,342,346,349,358,365,371,393,422,453,455,462,467,469,470,471,476,486,490,494,495,497,499],convex:[42,335,376],convinc:[7,12],cook:9,cooki:7,cool:[7,158,235,297],cooordin:191,cooper:[5,7],coord123:116,coord1:[3,116,206,210,211],coord2:[3,116,206,210,211],coord3:[3,116,206,210,211],coord:[],coordb:440,coordbb:440,coordiat:363,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,94,104,105,107,115,116,118,136,142,151,157,163,165,166,168,172,190,191,192,193,194,195,197,200,205,206,209,210,211,214,215,216,217,218,219,220,221,224,226,227,229,231,234,235,236,237,238,239,240,252,254,255,257,258,259,261,262,263,276,279,280,281,284,285,286,296,297,299,301,302,303,308,311,312,313,314,316,324,325,326,333,334,336,337,358,363,364,365,370,371,372,375,376,394,440,464,469,470,471,472,474,477,479,483,490,495,496],coordn:[116,206],coorind:105,copi:[0,3,4,8,11,12,15,17,40,121,193,326,365,384,432,467],copper:462,coproccesor:16,coprocessor:[1,4,7,9,16,17,370,482],coproprocessor:17,copy_arrai:8,copyright:[7,8,284],coral:194,core:[],core_shel:150,coreshel:[6,9,380,387,389],cornel:[6,174,481],corner123i:115,corner123x:115,corner123z:115,corner1i:115,corner1x:115,corner1z:115,corner2i:115,corner2x:115,corner2z:115,corner3i:115,corner3x:115,corner3z:115,corner:[3,6,40,115,193,335,336,358,457,469],cornflowerblu:194,cornsilk:194,corpor:16,corr:386,correct:[3,6,9,11,12,16,17,59,87,88,103,104,112,118,150,155,162,193,220,231,233,239,255,256,276,284,286,289,325,331,335,355,365,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,457,458,460,461,462,469,484,487,490],correction_max_iter:203,correctli:[3,8,9,11,17,71,81,103,104,145,146,147,149,151,153,154,155,156,157,160,161,164,191,194,200,221,226,229,240,249,255,256,292,299,302,311,313,332,335,365,366,370,389,417,422,466,467,469,479,494,496],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,87,97,98,111,114,115,116,117,120,121,129,132,133,134,135,136,138,139,140,142,145,146,155,162,167,174,175,176,177,178,179,180,182,183,185,186,188,191,193,194,198,199,200,206,208,209,210,211,213,216,218,220,227,229,230,234,239,242,243,251,252,253,255,257,258,259,260,261,262,263,264,265,269,272,274,275,276,278,281,282,286,291,299,301,302,317,319,321,330,331,332,334,335,336,338,340,341,342,343,345,346,349,351,356,360,362,364,365,371,372,374,378,379,380,381,382,383,384,385,386,387,390,391,393,394,395,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,419,420,422,424,425,426,427,429,430,432,433,434,435,440,441,442,451,452,453,454,455,457,458,460,461,462,464,466,467,469,470,472,482,483,484,486,487,490,495],correspondingli:[416,417,478],cosin:[],cosineshift:27,cosmo:[233,238],cossq:[],cost:[1,6,10,11,12,17,39,41,71,111,120,143,167,193,194,206,210,211,214,215,216,228,255,291,326,355,356,368,387,407,411,422,424,451,466,478],costheta0:[451,453,455,458],costheta:430,costli:[11,88,233,366],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,94,105,107,111,114,116,148,158,163,165,181,191,193,194,198,199,206,207,210,214,220,229,238,288,289,290,294,297,299,301,314,315,321,325,326,327,331,335,337,339,347,352,354,361,363,366,370,373,397,401,402,432,433,465,466,467,469,471,473,476,477,485,490,495,496],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,88,109,110,118,143,169,173,290,292,327,355,356,363,370,378,380,381,382,383,386,387,388,389,390,395,399,400,402,407,411,415,418,424,427,432,433,435,440,450,455,456,458,461,474,481,487,490,494],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,116,118,119,156,166,172,200,201,204,206,209,210,211,213,214,221,226,228,231,237,255,269,285,302,317,318,335,356,363,364,365,367,370,397,401,424,487,495],counter:[332,464,475,477,483],counteract:231,counterbal:235,counterbalanc:29,counterpart:[191,299,464],counterproduct:18,coupl:[],courant:304,cours:[3,8,128,130,162,191,198,199,232,298,311,325,331,333,334,336,337,356,416,442,466,469,482,490,495,497],courtesi:358,cov:440,coval:[6,29,395,419,440,490],covari:233,cover:[6,71,188,194,203,242,395,405,457],coverag:[71,210],cpc:238,cpp:[1,3,6,8,9,11,12,13,87,191,198,199,229,302],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,194,208,224,240,327,353,356,370,384,450,464,482,483,486,487,488,495],cpuremain:487,cr2:167,cr3:167,crack:[4,366],crada:[5,7],crai:[5,7,13,18,191],crash:[3,12,366,490],craympi:370,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:203,create_faceset:203,create_group:192,create_nodeset:203,createatom:[],creation:[],crimson:194,critchlei:284,criteria:[3,118,169,193,194,215,216,217,250,363,429,457,471,474,495],criterion:[12,41,123,166,168,171,204,214,217,231,269,291,304,332,337,363,365,386,395,399,440,474,483,484],criterioni:483,critic:[6,48,49,253,321,326,363],crmax:71,crmin:71,cross:[3,12,22,71,89,146,176,191,193,205,210,216,220,252,254,276,299,307,311,313,322,329,341,358,365,382,391,392,393,400,401,402,407,409,411,430,435,437,439,453,455,462,469,473,479,497],crossov:1,crossterm:469,crozier:[0,7,13],crucial:289,crystal:[4,6,13,73,108,280,281,324,358,366,473,487,490],crystallin:[6,104,281,358,454,490],crystallis:321,crystallogr:[120,167],crystallograph:[358,487],crystallographi:[120,167,358],cs1:167,cs_chunk:6,cs_im:[40,469],cs_re:[40,469],csanyi:[142,431,441],cscl:419,csequ:6,csh:[11,12,384],cshrc:[11,12],csic:[394,451,453,455,458],csinfo:6,csisi:[394,451,453,455,458],csld:[],cst:393,cstherm:6,cstyle:466,csvr:[],ctcm:[371,393],ctemp_cor:224,cterm:303,ctr:9,ctype:11,cu1:167,cu2:167,cu3au:419,cube:[6,41,166,171,214,224,335,358,490],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:377,cummul:[3,6,212,215,216,217,219,228,233,239,241,314,317,318,319,320,322,329,401,487],cumul:[6,204,206,209,210,211,225,231,239,253,255,260,269,299,300,365],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,103,104,110,118,119,132,143,148,156,158,164,166,169,172,190,191,192,193,194,195,198,199,203,206,210,211,212,214,215,216,217,218,219,220,221,225,226,229,231,233,236,237,239,245,252,255,256,261,262,263,269,274,275,276,278,284,290,291,293,296,297,298,299,302,303,304,305,306,307,308,310,312,313,314,317,318,319,325,326,329,330,331,332,333,334,336,337,339,353,354,355,356,359,360,362,363,364,365,370,376,377,384,386,390,393,395,396,399,402,403,406,416,417,419,420,421,424,430,432,433,436,437,438,439,442,453,455,456,459,464,465,466,467,469,470,471,472,473,475,476,477,479,481,483,484,486,487,495,496,497,498,499],curv:[6,168,231,281],curvatur:[398,434,462],custom:[],cut0:467,cut1:478,cut2:478,cut:[],cuthi:[280,292],cutinn:[379,416,417],cutlo:[280,292],cutmax:430,cutoff1:[383,390,407,411,415,418,427,435],cutoff2:[378,380,381,383,389,390,407,411,415,418,427,435],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,92,108,110,117,118,142,166,169,171,216,217,222,280,289,290,292,294,296,299,314,327,331,335,337,353,355,356,363,366,367,368,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,387,388,389,390,391,392,393,394,395,396,397,398,400,401,402,403,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,432,433,434,435,440,441,442,443,444,445,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,467,471,474,478,490,495],cutoff_glob:376,cutoff_inn:376,cutoffa:394,cutoffc:394,cuu3:393,cval:167,cvd:321,cvel:303,cvff:[],cwiggl:[3,252,331,334,336,495],cyan:[2,193,194],cycl:[3,231,253,255,256,260],cyclic:[3,188],cygwin:12,cylind:[3,4,71,193,206,237,285,332,335,472],cylindr:[6,237,311,332],cypress:370,cyrot:377,cyrstal:281,d3q15:242,d3q19:242,d_double_doubl:15,d_e:326,d_flag2:288,d_flag:288,d_name:[115,191,288,316,479],d_single_doubl:15,d_single_singl:15,d_sx:288,d_sy:288,d_sz:288,daan:324,dai:12,daili:12,daivi:276,damag:[],dammak:294,damp:[3,6,197,202,239,240,241,246,255,256,260,286,289,290,294,299,317,318,330,332,333,362,363,365,378,380,382,387,390,395,399,407,415,427,435,450,456,483,490],damp_com:240,damp_drud:240,dampen:[299,490],dampflag:[332,399],dan:17,danger:[3,12,231,337,391,487],dangl:171,daniel:9,darden:[356,390],darkblu:194,darkcyan:194,darken:193,darkgoldenrod:194,darkgrai:194,darkgreen:194,darkkhaki:194,darkmagenta:194,darkolivegreen:194,darkorang:194,darkorchid:194,darkr:194,darksalmon:194,darkseagreen:194,darkslateblu:194,darkslategrai:194,darkturquois:194,darkviolet:194,dasgupta:290,dash:[399,486],dat:[6,91,188,203,465],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,300],dataset:300,datatyp:3,date:[0,6,12,13,190,432,433,495],datom1:117,datom2:117,datom3:117,datom4:117,datum:[3,6,42,65,68,69,79,93,110,117,191,207],davenport:418,davi:331,david:[9,19,355,356,453,455],daw:[393,430],dbg:14,dcd:[3,6,7,191,192,193,194,195,282,470,474],ddim:190,deactiv:415,dealt:238,debug:[6,7,11,12,13,14,17,120,124,167,168,282,287,353,355,370,403,424,459,467,468,476,479,486,495],deby:[],decai:[92,387,462],decid:[3,6,12,16,71,252,288,299,327,484],decipher:358,declar:192,declin:314,decod:193,decompos:[87,441],decomposit:[3,5,7,18,62,203,282],decoupl:[6,490],decreas:[3,191,200,201,208,217,220,226,229,231,239,325,355],decrement:303,deepli:352,deeppink:194,deepskyblu:194,def:[12,13,467],defaul:61,defect:[6,70,166,422],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,174,175,176,177,178,179,180,182,183,185,186,187,188,189,190,191,192,193,194,197,198,199,200,201,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,220,221,224,225,226,229,230,231,234,237,238,239,240,241,242,250,252,254,255,256,257,258,259,260,261,262,263,265,266,267,270,272,273,274,275,276,277,278,280,281,282,284,285,286,288,290,292,297,299,300,301,302,304,308,312,314,316,317,318,319,320,322,323,324,326,328,329,331,332,333,334,335,336,337,339,340,341,342,343,344,345,346,349,350,351,353,355,356,358,360,362,363,364,365,366,367,368,369,370,372,373,374,375,376,378,379,380,381,382,383,384,385,387,388,390,391,392,394,395,397,398,399,400,401,402,403,405,407,408,409,410,411,412,413,414,415,416,417,418,422,423,424,425,426,427,429,430,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,466,467,469,470,472,473,474,475,478,479,480,481,483,484,486,487,490,491,492,493,494,495,496],definit:[2,3,6,8,12,13,78,80,118,142,194,206,207,208,209,210,211,212,220,237,260,300,316,328,331,334,336,338,350,353,364,373,377,385,395,405,430,437,439,441,457,467,469,471,478,480,494,495],defint:487,deform:[],deg2theta:167,deg:490,degener:[3,284],degrad:[8,18,281,356,478],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,93,95,97,98,100,102,103,108,114,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,161,167,168,174,175,178,179,186,188,190,193,206,217,224,231,233,234,239,240,245,255,256,260,261,262,263,274,275,276,278,282,284,298,299,302,317,318,319,324,340,342,346,349,351,363,390,393,401,479,487,490,496],degress:[148,206],del:483,delai:[3,6,12,366,392,487],deleg:402,delet:[2,3,7,8,12,54,57,60,63,166,171,172,197,206,207,209,210,211,212,215,217,228,231,255,300,317,318,337,339,354,364,366,369,424,449,469,470,471,472,480,481,486,491,493,495,496],delete_atom:[],delete_bond:[],delete_el:203,deli:190,delimit:[467,495],deloc:[256,395,440],delr:419,delt_lo:483,delta:[],delta_1:377,delta_3:377,delta_7:377,delta_conf:3,delta_ij:[419,430],delta_mu:3,delta_pi:377,delta_r:430,delta_sigma:377,delta_ua:376,delx:190,delz:190,dem:376,demand:294,demo:11,demon:279,demonstr:[289,419],den:285,dendrim:401,denniston:[9,242,244,245,246,281],denomin:[7,173],denot:[120,224,240,281,292,294,387,400,402,433,437,439],dens:[71,217,395],densiti:[3,6,7,9,18,40,41,59,101,118,128,142,154,166,168,198,199,203,206,210,211,214,220,229,242,245,248,249,281,285,286,290,326,331,358,360,364,371,377,393,419,420,421,430,434,440,444,446,447,448,469,478,479,487,494],density_continu:439,density_summ:439,depart:[0,7],departur:[253,289],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,93,104,110,111,114,115,116,117,121,142,145,151,155,156,162,168,169,174,175,176,177,178,179,180,182,183,185,186,187,188,190,191,193,194,197,198,199,200,201,204,206,208,209,210,212,213,214,216,218,220,226,227,230,233,234,235,237,239,240,242,244,245,252,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,280,291,294,296,299,301,302,308,314,317,318,319,321,323,325,326,328,330,331,334,335,336,337,339,340,341,342,343,345,346,349,351,356,358,363,364,366,367,368,370,371,372,374,375,377,378,379,380,381,382,383,384,385,386,387,388,390,391,393,394,395,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,419,420,422,423,425,426,427,429,430,432,433,434,435,440,441,442,450,451,452,453,454,455,456,457,458,460,461,462,464,466,469,471,472,475,479,481,483,486,487,489,495,496],dependend:6,depflag:12,dephas:[464,483],depos:221,deposit:[],deprec:[290,432],depth:[51,146,193,326,398,434],dequidt:9,der:[87,109,385,386,415,432,433,461,490],deriv:[6,7,8,9,38,56,63,87,142,162,188,207,218,220,231,239,252,255,257,258,259,260,261,262,263,280,286,290,294,323,324,326,331,332,335,362,364,372,377,385,390,395,396,400,409,413,414,419,422,432,433,450,452,461,490],derjagin:461,derlet:280,descend:194,descent:[7,362],descib:[40,193,290],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,112,115,118,120,132,142,143,146,147,148,152,153,156,159,161,162,166,167,168,170,171,180,185,188,191,192,197,198,199,206,207,208,209,210,211,212,214,217,218,219,220,221,223,224,232,233,236,237,238,239,240,241,242,244,245,246,250,254,255,256,260,268,277,280,282,287,288,289,290,291,292,299,303,311,314,315,316,317,318,319,320,321,322,323,324,329,331,332,334,339,355,356,358,361,362,363,364,365,369,372,373,375,376,378,379,380,382,383,384,385,386,387,390,393,395,396,398,399,400,402,407,408,409,410,411,412,413,414,415,416,417,418,419,422,423,429,430,431,432,433,434,435,440,441,442,449,450,451,452,453,454,455,456,458,460,461,462,464,466,467,469,470,471,472,473,479,482,483,486,495,496,497],descript:[],descriptor:[142,191,403],deserno:356,design:[0,3,6,7,8,9,11,13,14,15,17,120,150,153,167,203,217,223,224,255,256,280,281,300,321,326,373,374,375,376,379,382,387,389,395,415,416,417,420,421,430,433,452,478],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,114,119,143,150,168,181,190,206,212,218,220,229,231,232,239,240,241,245,255,276,284,285,286,287,290,294,299,302,314,317,318,319,320,325,332,347,352,355,356,358,361,363,364,365,391,393,401,416,417,451,453,455,465,466,467,469,473,478,483,484,486,487,495,496,497],desk:7,desktop:[4,6,7,10,12,193],despit:490,destabil:377,destre:349,destroi:[11,39,215,216],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,94,103,105,107,109,111,113,114,116,119,121,142,143,145,146,147,148,151,161,162,163,165,168,169,172,173,176,187,190,191,193,194,197,198,199,203,206,207,208,209,210,212,214,216,217,218,219,220,221,229,231,232,233,234,236,237,239,241,242,246,252,253,254,255,256,257,258,259,260,261,262,263,267,269,274,275,276,277,278,281,284,285,286,288,289,291,292,293,299,302,314,317,318,319,320,321,322,324,325,326,327,328,329,330,337,339,341,350,355,356,359,363,364,366,367,370,371,372,373,375,376,377,379,381,382,383,384,385,386,387,390,391,395,396,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,417,418,419,423,424,429,432,433,434,440,441,442,450,457,460,461,467,469,470,471,472,474,475,478,479,481,484,487,488,495,496,499],detect:[2,3,12,42,61,63,86,92,230,285,325,365,386,401,406,464,466,469,480,483,495],determ:370,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,87,103,109,111,114,120,121,129,143,156,157,166,167,168,190,191,193,194,195,196,200,201,202,205,206,207,208,209,210,211,212,213,214,218,220,221,224,226,231,234,235,237,239,240,245,250,252,253,255,261,262,263,274,275,276,278,280,282,286,289,296,297,298,299,300,301,304,306,308,314,317,318,319,321,327,328,331,332,333,334,335,336,337,350,355,356,358,364,366,367,370,372,373,381,386,390,392,393,397,399,402,403,411,419,422,424,433,434,440,449,452,456,461,466,469,470,472,474,476,479,483,485,486,488,494,495,496],detil:110,devan:[9,435],devanathan:455,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,236,260,284,289,290,293,372,377,395,421,422,440,458,471],devemi:9,deviat:[253,260,280,397],deviator:9,devic:[1,3,12,15,17,236,370],device_typ:370,devin:[291,386],devis:421,dfactor:193,dff:490,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,356],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,293,422],dhi:[59,190,220,285],dhug:[253,289],dhugoniot:[253,289],dia:419,diagnost:[],diagon:[3,6,83,142,143,144,218,255,286,299,329,437,439],diagonalstyl:441,diagram:[41,120,167,187,214,282],diallo:401,diam:[193,194,285,364],diamet:[3,6,40,42,115,168,191,193,194,198,199,239,285,299,314,330,332,364,376,385,398,399,405,409,434,457,461,469,470,479],diamond:[358,395,419],diamter:[40,285],dick:6,dicsuss:252,dictat:[204,253],did:[3,12,363,391,392,393,399,424,453,455,477],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,164,328,355],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,92,95,97,98,122,142,145,146,147,148,149,151,154,155,156,157,158,160,161,162,168,169,171,176,187,188,190,191,193,194,197,199,202,204,206,209,214,215,216,217,218,219,220,224,230,231,232,233,234,235,236,239,240,242,252,255,256,257,258,259,261,262,263,265,267,270,272,273,274,275,278,280,282,284,286,289,290,291,294,297,299,302,303,311,312,314,317,318,319,322,323,324,326,329,330,331,332,335,339,340,350,352,354,355,356,358,359,361,362,364,365,367,368,369,370,371,372,377,381,382,384,385,386,391,393,395,398,399,400,402,405,407,408,410,411,418,419,420,421,423,424,426,430,432,433,434,435,436,437,439,440,441,442,450,451,452,453,455,457,458,461,463,464,466,467,469,471,472,473,474,477,478,479,481,483,484,486,487,488,490,494,495,496,497],differenti:[1,3,6,29,188,355,387,430,454],difficult:[218,282,370,401,478],difficulti:[92,108,302,432],diffract:[],diffus:[],digit:[2,3,194,339,422],dih_table1:188,dih_table2:188,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:216,dihydrid:395,dij:302,dilat:[],dim1:3,dim2:3,dim:[3,59,71,145,149,150,151,154,155,156,157,158,160,168,190,210,220,237,332,358,419,472,494,495,496],dimdim:495,dimems:281,dimens:[],dimensinon:71,dimension:[3,39,92,114,120,142,145,148,149,150,151,154,155,156,157,158,160,167,189,206,210,254,281,326,358,361,365,430,469,479],dimensionless:[106,123,124,126,129,131,133,138,142,326,356,441,461],dimentionless:137,dimer:[6,299,419],dimgrai:194,dimstr:[41,214],dinola:[286,317],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,191,316,490],dir1:480,dir2:480,dir:[1,3,4,8,9,11,12,253,280,289,313,430,432,433,467,480,495],dirac:142,direc:430,direct:[],directli:[3,6,8,9,11,12,87,115,142,144,191,192,193,200,226,233,237,242,281,300,318,330,332,333,334,335,358,362,370,371,372,378,380,381,387,390,393,395,407,411,424,427,435,449,467,479,480,481,487,495],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,195,219,238,284,290,293,310,314,323,324,365,369,371,372,377,384,386,387,393,394,396,403,404,415,419,420,421,422,426,430,431,432,433,440,441,451,453,454,455,458,467,469,470,471,480,495],disabl:[3,12,16,326,406,467,482,495],disadvantag:[6,214],disallow:[191,220,255],disappear:471,discard:[2,3,41,71,208,210,214,327,335,466,471,472],discontinu:[9,188,363,413],discourag:419,discov:[13,327],discret:[6,8,40,42,193,194,239,242,376],discuss:[],disk:[6,84,85,92,161,189,221,231,285,467],disloc:[70,422],disord:[39,70,422],disp:[],dispar:434,disperion:[390,411],dispers:[3,6,7,9,166,281,355,356,381,390,411,416,424,433,452,458],displac:[],displace_atom:[],displace_box:59,displacemet:472,displai:[11,13,22,37,44,55,176,187,191,193,341,350,384,450],dispters:3,disregard:422,dissip:[6,232,239,281,323,324,379,391,399,416,417,450],dissolut:215,dist:[6,69,91,110,119,191,282,298,392,449,464,496],distanc:[],distinct:[6,224,296,355,434],distinguish:[6,86,142,245,376,395,468],distort:371,distrbut:371,distribut:[],distro:[113,384,429,430],ditto:[8,12,14,15,16,17,18,42,117,216,462,467],div:8,divd:119,diverg:[3,12,39,299,324,471,490,497],divid:[3,6,16,41,91,114,119,128,130,143,165,166,176,187,194,206,207,209,214,220,280,322,329,334,355,363,365,396,433,440,458,478,486,495],divis:[6,242,377,405,415,466,487,495],dl_poli:[6,7],dlambda:162,dlammps_async_imd:236,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,193],dlammps_gzip:[3,12,191,193,325,469,470,474],dlammps_jpeg:[3,12,193],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,193],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,191],dlen:479,dlmp_intel_offload:[12,16],dlo:[59,190,220,285],dlopen:6,dlvo:[7,385,461],dm_lb:242,dmax:[314,361],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,94,103,105,106,107,109,111,113,114,116,119,121,143,146,147,148,161,163,165,168,169,170,176,187,190,191,192,193,194,195,197,198,199,204,205,206,207,208,209,210,211,212,221,231,239,240,250,255,256,261,262,263,267,274,275,276,277,278,285,288,299,311,314,317,318,319,328,332,335,337,339,341,350,354,363,364,365,370,371,372,375,376,384,386,387,393,394,396,401,402,404,405,419,420,421,424,426,429,430,431,441,450,451,453,455,457,458,467,469,470,471,472,474,477,478,479,486,487,495,496,497,498],docuement:434,dodd:[42,376],dodgerblu:194,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,39,41,42,50,54,56,59,62,63,67,70,71,72,87,88,91,105,112,118,119,120,144,146,148,150,151,156,158,162,167,168,169,170,172,174,176,181,187,188,190,191,192,193,194,197,203,204,206,210,213,214,216,217,218,220,224,226,228,231,232,235,237,239,240,242,245,251,255,256,257,258,259,261,262,263,274,275,276,277,278,286,287,288,292,294,297,299,314,317,319,321,322,326,329,330,331,334,335,336,337,342,343,344,346,347,349,354,355,356,357,358,364,365,366,371,372,373,374,375,376,377,379,381,382,383,385,386,387,388,390,391,392,393,394,395,397,398,399,400,402,403,404,405,406,409,410,412,413,414,416,417,419,420,421,422,424,430,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,456,457,458,460,461,462,464,465,466,467,469,470,471,472,473,476,477,479,480,481,482,483,486,487,490,495,499],doegenomestolif:7,doesn:[3,7,8,12,168,191,204,210,211,311,364,366,370,372,386,394,404,432,433,451,453,454,455,458,469,471],dof:[3,8,114,146,147,148,161,206,299,496],dof_per_atom:[148,206],dof_per_chunk:[148,206],doff:[364,469],doi:[6,219],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,120,157,167,170,190,192,193,194,197,204,214,218,220,221,235,238,242,255,256,282,294,299,326,331,332,355,356,365,370,392,424,464,466,469,473,486],domin:[1,395,483],don:[0,8,11,12,13,118,171,200,226,240,288,335,419,440,467,469],donadio:318,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,162,165,168,171,188,191,193,194,203,204,206,208,209,210,211,212,214,215,216,217,218,220,221,229,231,236,237,239,240,247,255,261,262,263,274,275,276,278,279,281,282,283,288,296,299,300,302,314,317,318,319,321,323,324,337,339,354,355,356,363,365,366,369,370,372,381,393,402,403,404,411,417,418,419,424,432,449,452,457,464,465,466,467,470,473,474,477,487,488,490,495,496],donor:401,dot:[143,164,200,226,234,254],doti:[377,430],doubl:[1,2,3,6,8,9,11,12,14,15,16,17,39,87,220,229,287,335,339,354,356,369,370,377,396,400,422,432,433,465,469,473,477,482,495,496],dover:203,down:[3,6,7,8,11,39,71,218,231,239,314,330,370,395,424,440,468,488],downhil:[361,362],download:[5,7,8,9,11,12,13,17,236,403,431],downsid:6,downward:296,dozen:[8,12,109,197,432,433],dpack_arrai:12,dpack_memcpi:12,dpack_point:12,dpd:[],dpde:248,dproduct:373,dr_ewald:[120,300],drag:[],dragforc:242,drai:[253,289],drain:[235,330,363],dramat:[59,190,215,216,217,218,220,255,314,317,318,356,370,424,440,466],drautz:377,draw:193,drawback:288,drawn:[42,191,193,194,232,464],drayleigh:[253,289],dreid:[],drfourth:106,drho:[115,371,393],drift:[6,104,106,232,233,239,240,251,297,314,478,486,490],drive:[11,12,201,218,220,234,255,280,286,299,333,365],driven:[6,180],driver:[6,12,14,15,197,229,236],drop:[3,194,391],droplet:402,drsquar:106,drude:[],dry:228,dsecriptor:403,dsf:[],dsmc:[],dstyle:285,dt_collis:242,dt_lb:242,dt_md:242,dt_srd:314,dtilt:[59,220],dtneb:483,dtqm:289,dtype:[117,216],dual:[16,17,314,370],dudarev:167,due:[1,3,6,9,10,12,16,17,19,40,54,57,58,61,66,70,71,74,75,81,86,88,89,90,94,103,104,105,106,107,112,118,120,128,142,143,145,146,147,149,151,154,155,156,157,158,160,161,163,167,168,171,172,191,193,197,200,201,209,213,215,216,217,218,219,220,221,226,227,228,229,232,233,236,237,239,240,241,242,245,246,247,251,252,253,254,255,260,269,280,283,285,297,298,299,301,311,313,314,315,317,318,319,320,321,323,324,326,330,331,333,334,335,337,356,361,363,365,366,367,388,391,393,397,398,402,416,417,424,430,432,434,435,449,452,453,455,459,461,462,464,466,469,470,471,478,483,486,487,488,490,495,496],duffi:326,duin:[9,290,295,432,433],duke:356,dummi:[12,29,454],dump1:474,dump2:474,dump2vtk_tri:136,dump:[],dump_atom:8,dump_custom:8,dump_h5md:192,dump_modifi:[],dumpcustom:8,dumptimestep:474,dunbrack:[6,20,174,382,481],dunweg:[239,241],duplic:[2,3,14,15,17,41,42,169,214,233,280,469,494],dupont:[5,7,13],durat:[37,55,145,146,147,149,150,151,153,154,155,156,157,160,161,187,194,206,231,294,326,350,399,450],dure:[2,3,6,8,9,12,16,17,38,39,41,56,71,87,128,130,144,150,169,172,188,191,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,222,225,226,227,228,229,230,231,232,233,234,235,236,237,239,240,241,242,243,244,245,246,247,248,249,251,252,254,255,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,307,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,356,363,365,369,370,391,415,422,424,433,452,464,465,467,469,472,474,476,477,479,481,483,484,487,488,495,498,499],dvector:8,dvlo:461,dvx:6,dx_lb:242,dy3:167,dyamic:12,dyanam:6,dyanmic:483,dynam:[],dynamo:[5,371,393,419],dyne:494,dyre:412,dysam:472,e28637:29,e_1:377,e_2:377,e_b:396,e_e:395,e_hbond:401,e_i:[6,377,396],e_j:[6,377],e_k:[377,395],e_kl:6,e_lj:[372,390],e_n:[377,395],e_nn:395,e_pr:395,e_rebo:372,e_tors:372,e_tot:422,e_vol:422,eaa:340,eaat:175,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,66,67,68,70,71,72,73,74,75,76,77,78,80,81,83,85,87,89,90,92,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,111,112,113,114,115,116,117,118,119,120,121,122,136,142,143,144,146,147,148,149,150,151,152,155,156,157,158,160,161,162,163,164,165,166,167,168,171,172,174,175,176,177,178,179,180,181,182,183,185,186,187,188,190,191,192,193,194,195,196,197,198,199,200,201,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,245,246,247,248,249,251,252,253,254,255,257,258,259,260,261,262,263,264,265,266,267,269,270,271,272,273,274,275,276,277,278,280,281,282,283,284,285,286,287,288,290,291,292,294,296,299,300,301,302,303,307,308,310,311,312,313,314,315,316,317,318,319,321,324,325,326,327,328,329,330,331,332,334,335,336,337,339,340,342,343,344,345,346,347,349,350,351,354,355,356,358,362,363,364,365,366,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,395,396,397,398,399,400,401,402,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,422,423,424,425,426,427,429,430,432,433,434,435,436,440,441,442,443,444,445,446,447,448,449,450,451,452,455,456,457,458,459,460,461,462,463,464,466,467,469,470,471,472,473,474,476,477,478,479,481,483,484,486,487,488,489,490,494,495,496,497,499],eacn:[41,214],eam0d:281,eam3d:281,eam:[],eam_databas:13,eam_gener:13,eangl:487,earli:[41,206,209,210,211,212,214,293,300],earlier:[7,8,12,59,194,365,399,419,424,483],earliest:483,earth:395,easi:[6,7,8,9,11,13,87,143,191,198,199,200,201,210,213,226,234,235,237,239,2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,319,322,323,324,326,328,329,331,334,336,337,339,354,358,363,365,366,367,369,370,386,391,397,398,401,416,422,423,430,432,433,434,436,437,438,440,441,442,452,457,458,462,465,466,467,469,471,472,476,477,480,483,485,487,495,496],equat:[3,6,7,8,9,91,108,114,120,167,176,187,197,218,224,225,233,239,240,242,245,253,254,255,256,260,276,280,282,289,290,294,302,314,322,326,329,331,332,334,336,349,355,356,385,390,391,395,396,399,404,416,417,419,424,434,437,439,444,445,447,448,462,490],equi:256,equidist:254,equil:[3,290,359,476,499],equilater:479,equilibr:[3,4,5,6,7,9,59,91,168,197,204,207,217,218,231,253,255,256,276,277,289,290,291,292,322,323,324,329,386,387,432,433,465,479],equilibria:329,equilibribum:[215,216],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,151,152,175,177,218,220,231,232,233,240,242,255,260,276,289,290,294,298,302,303,311,314,321,322,324,329,340,342,346,349,386,419,426,440,490],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:203,equival:[6,12,13,29,59,61,126,127,135,140,166,170,194,209,212,218,220,231,239,255,276,286,298,299,334,391,395,440,453,455,469,472,477,478,487,490],equlibrium:6,equliibr:[290,292],er3:167,eradiu:[40,115,395,469],eras:[301,323],erat:[220,417],erc:387,erfc:[387,407,424],erforc:115,erg:494,erhart:[204,393,453,455],ermscal:373,ernst:9,eror:3,eros:419,erose_form:419,erot:[],errata:[453,455],erratum:331,erron:3,error:[],erta:399,ervel:[115,469],escap:[221,490],especi:[8,11,16,156,168,197,204,214,231,289,294,297,298,370,466],espresso:[9,293],essenti:[8,11,12,27,88,130,149,150,151,154,155,156,157,158,160,177,207,260,281,330,356,372,387,407,455,474,487],essex:29,establish:[87,235],estim:[1,3,6,10,12,38,41,56,91,143,203,214,225,253,314,321,355,356,361,424,433,452,483,487],esu:494,esub:419,eta:[6,242,255,289,290,292,330,394,396,398,430,454,458,494],eta_dot:255,eta_ij:430,eta_ji:396,etag:[40,469],etail:487,etap:255,etap_dot:255,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,95,111,112,115,117,143,145,148,149,150,151,152,154,155,156,157,158,160,162,168,170,171,172,181,191,193,194,197,198,203,204,205,206,209,210,211,212,215,216,220,221,229,231,232,239,255,285,296,300,326,327,335,339,354,355,363,364,365,366,368,393,394,402,415,417,422,428,432,433,451,453,455,458,464,467,469,470,471,476,478,479,483,485,486,487,488,490,494,495,497,499],ethernet:18,etol:[363,365,464,483],etot0:289,etot:[6,95,97,98,112,143,154,194,224,240,253,289,486,487],eu2:167,eu3:167,euler:[363,365],eulerian:203,euqat:443,europhi:242,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,87,88,91,109,119,142,144,148,158,166,168,190,191,193,194,198,199,200,201,203,205,206,207,208,209,210,211,212,213,220,226,232,234,235,237,238,239,240,281,287,290,301,304,308,317,318,319,328,331,334,336,337,339,355,356,361,363,370,422,424,430,436,438,440,452,464,465,467,471,472,474,476,477,478,479,483,485,487,495,496],evalut:[339,467],evan:[156,276],evanseck:[6,20,174,382,481],evapor:[],evaul:[8,363],evdwl:[109,432,433,487],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,121,169,170,184,188,191,194,197,198,199,204,205,206,209,210,211,212,214,215,216,218,220,221,224,237,240,253,255,256,281,294,296,299,300,310,314,322,326,329,331,335,337,348,355,361,363,365,370,375,395,396,399,402,424,434,458,459,469,470,472,474,475,476,478,479,481,484,486,487,488,490,499],evenli:[3,41,143,188,214,242,405,459],event:[],eventu:[3,6,12,15,170,290,483],ever:[54,56,238,314],evera:[385,398,434,450],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,115,121,130,156,171,191,192,193,194,195,197,198,199,200,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,225,228,229,231,233,235,236,237,242,243,251,255,256,260,279,280,281,285,286,287,288,289,290,291,292,294,296,297,299,300,302,303,314,316,317,318,319,320,321,322,325,326,327,328,329,337,339,354,356,365,366,367,370,391,392,402,415,432,433,440,446,463,464,465,469,471,473,474,476,477,478,483,484,485,487,495,499],everyth:[8,109],everywher:[118,409],eviri:395,evolut:[233,242,282,464],evolv:[242,282,327],ewald:[2,3,5,6,7,8,12,88,112,120,143,327,355,356,363,378,380,381,387,390,395,407,411,427,435,450,452],ewald_disp:390,ewalddisp:3,exact:[22,41,44,71,124,162,171,176,214,217,232,233,239,240,241,285,294,295,314,326,341,355,384,471,476,483,495,497,499],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,91,118,146,152,159,168,188,198,199,209,214,220,225,232,239,240,241,256,268,269,277,281,289,314,319,320,333,370,384,391,393,399,402,405,416,424,452,471,472,479,483,495],exager:490,examin:[6,8,9,17,217,281],examp:[467,495],exampl:[],exce:[3,6,16,17,18,41,58,71,170,205,206,209,210,211,212,214,218,220,225,228,255,281,296,300,305,306,314,363,370,469,495],exceed:[3,41,59,214,220,255,314,477],excel:395,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,110,111,114,119,143,145,146,147,148,149,150,151,152,154,155,156,157,158,159,160,161,168,172,174,175,176,177,178,179,180,182,183,185,186,187,188,190,191,194,197,200,206,207,209,213,214,218,220,227,230,231,234,237,239,241,255,256,257,258,259,260,261,262,263,264,265,268,269,272,274,275,276,277,278,282,291,292,299,301,302,311,314,317,319,320,326,330,334,337,339,340,341,342,343,345,346,349,350,351,355,356,358,360,364,365,366,368,369,370,371,372,374,378,379,380,381,382,383,384,385,386,387,389,390,391,393,394,395,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,417,420,425,426,427,429,432,433,434,435,442,450,451,452,453,454,455,457,458,460,461,462,464,466,467,469,471,472,474,477,478,479,480,481,483,487,490,494,495,496,498],excess:[208,395],exchang:[2,3,6,8,9,61,62,197,203,204,231,239,291,299,322,326,329,355,370,395,484],exchange:355,excit:[9,395],exclud:[3,6,9,12,16,17,63,71,114,142,148,155,156,172,191,206,210,215,216,243,251,284,297,299,321,332,337,363,364,366,379,399,402,416,417,424,449,481],exclus:[1,3,9,12,16,87,370,386,422,424,478,488],excurs:[255,464],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,169,193,236,293,339,354,357,369,465,467,477,480,483,495],exempl:440,exemplari:232,exemplifi:395,exert:[6,237,240,294,333,334,335,356],exhaust:[203,369,495],exhibit:[92,255,362,395,478],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,124,168,169,187,192,193,194,197,202,213,216,218,221,231,284,285,287,337,340,342,343,344,346,350,359,364,370,402,432,449,459,465,467,469,470,471,480,481,482,495,496,497],exit:[2,3,11,12,41,57,191,214,354,369,467,468,477,486,495],exlanatori:3,exp:[],expand:[],expans:[12,142,191,480,495],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,103,149,160,166,188,214,226,231,233,252,280,286,288,289,294,299,337,356,366,384,419,422,424,464,467,469,471,474,478,483,495],expens:[6,10,71,194,280,284,299,326,337,355,356,366,370,467],experi:[6,13,15,17,213,221,236,245,254,286,298,299,361,365,391,424,478,483],experienc:[6,12,244,245],experiment:[231,355,370,483],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,93,148,156,188,191,193,194,197,206,207,212,214,216,218,220,255,280,288,299,311,337,339,354,355,358,364,365,369,375,393,405,440,442,457,467,470,471,474,476,479,490,495,499],explan:[3,6,59,115,142,191,206,254,280,402,463,466,467,469,478],explanatori:[3,8,119,191,205,206,209,210,211,299,364,466,495],explantori:[3,295],explic:423,explicit:[6,9,11,22,44,77,87,115,118,162,176,198,199,220,305,306,341,360,372,373,377,382,384,393,395,406,416,456,463,466,470,473],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,111,114,145,155,158,166,168,174,175,177,178,179,180,182,183,185,186,188,191,194,200,210,213,220,227,230,232,234,239,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,288,289,291,299,301,302,317,319,320,326,330,334,340,342,343,345,346,349,351,364,370,371,372,374,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,396,397,398,399,400,401,402,405,406,407,408,409,410,411,412,413,414,415,416,420,422,424,425,426,427,429,434,435,442,443,444,445,446,447,448,450,451,452,453,454,455,456,457,458,460,461,462,469,471,472,478,479,481,482,488,490],explictli:[16,482],exploit:[9,15,17,282],explor:[120,167],expon:[3,290,292,393,398,401,415,423,435],exponenti:[87,430,451,458,462,483,495],expos:11,exposit:[203,391,392],express:[6,142,154,168,198,199,218,252,280,290,326,332,339,377,393,395,409,419,440,441,450,495],expressiont:377,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,95,98,99,109,111,119,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,197,200,201,204,212,213,219,222,226,229,230,231,233,234,235,237,239,241,253,255,260,269,280,281,297,298,299,301,303,308,311,313,317,318,319,320,321,323,324,326,328,331,335,336,398,419,422,433,434,441,486,487],extent:[1,3,41,42,45,57,71,166,170,191,202,210,214,237,333,336,355,358,372,436,438,452,466,469,472],exterior:[3,6,335],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,103,111,112,114,120,143,145,146,147,149,151,154,155,156,157,158,160,161,167,168,169,170,174,194,209,214,216,255,287,288,289,299,314,363,364,367,368,390,399,402,405,419,424,466,467,469,472,481,490,495],extract:[3,6,11,13,36,63,87,109,117,119,121,198,199,292,365,387,396,419,441,467,474,486],extract_atom:11,extract_comput:[11,467],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,193,208,218,220,255,324,395,454,490],extrema:415,extrins:203,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[164,328],f_a:[453,454,455],f_ave:119,f_c:454,f_f:455,f_fix_id:289,f_harm:324,f_i:[29,430],f_id:[6,71,119,121,191,197,205,206,207,208,209,210,211,212,250,316,328,487,495],f_ij:430,f_indent:212,f_int:323,f_j:29,f_jj:91,f_k:430,f_langevin:326,f_max:[289,294],f_msst:253,f_r:[240,453,454,455],f_sigma:377,f_solid:324,f_ss:6,f_temp:[],face:[3,6,57,59,71,156,166,170,202,210,211,331,333,334,335,336,358,398,419,434,469,472],face_threshold:166,facet:166,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,233,314,324,399,440,481],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,87,91,103,110,117,118,120,142,162,167,170,174,185,190,191,193,194,198,199,207,214,218,220,221,231,236,239,241,242,253,255,256,260,282,286,290,298,302,304,306,314,318,322,329,330,331,335,346,356,358,364,370,372,373,377,378,380,382,387,388,389,391,395,399,402,406,407,419,422,424,426,427,433,435,442,451,456,466,469,472,473,478,481,483,484,487,490,494,495],factori:[3,467],factoriz:355,fail:[3,11,12,59,172,218,221,355,363,365,389,433,467],failur:[123,437,468,495],fairli:[11,424,478,483],faken:73,falcon:236,fall:[3,6,194,209,285,467,495],fals:[86,337,339,440,495],fame:8,famili:[458,466],familiar:[0,11],fan:430,far:[3,6,12,17,57,59,61,86,191,194,195,214,215,216,218,221,255,280,298,299,314,331,342,346,361,365,366,457,467,469,474,487],farago:239,farrel:[453,455],farther:191,fashion:[6,8,41,71,168,194,197,198,199,204,210,214,216,221,231,233,237,252,253,255,257,258,259,260,261,262,263,271,274,275,276,277,278,288,289,291,299,303,307,313,316,324,326,330,331,332,334,336,365,402,416,472,481,495,498],fasolino:404,fast:[6,7,9,12,13,17,39,191,266,289,327,355,356,379,416,417,422,450,452,471,476,478,487,496,499],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,106,111,114,145,155,174,175,177,178,179,180,182,183,185,186,188,191,194,200,213,214,220,227,230,234,238,239,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,286,290,291,299,301,302,314,317,319,321,323,326,330,334,340,342,343,345,346,349,351,355,356,367,368,370,371,372,374,377,378,379,380,381,382,383,384,385,386,387,390,391,393,394,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,420,425,426,427,429,434,435,442,450,451,452,453,454,455,457,458,460,461,462,464,472,478,482,490],fastest:[1,6,14,17,156,210,326,327,370,466],fatal:[3,486],fault:[70,433],faulti:12,fava:398,favor:217,favorit:7,fbmc:321,fcc:[],fcm:[271,495],fdirect:224,fdotr:403,fdti:87,fe2:167,fe3:167,fe_md_boundari:203,featu:8,featur:[],fecr:393,feedback:[7,236],feel:[7,236,237,245,280,335,337,365,424],felling:421,felt:335,femtosecond:494,fene:[],fennel:[387,407],fep:[],ferguson:[6,174,481],fermi:[1,12,15,154,370,455],fermion:[9,395],fernando:418,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,195,205,206,207,209,210,211,212,240,255,285,288,290,302,328,355,363,364,365,372,440,466,469,474,478,480,488,495,497],fewer:[1,3,11,15,16,61,245,478],fewest:3,fextern:229,feynman:282,fff:467,ffield:[386,396,432,433,440],ffmpeg:[3,12,193],ffplai:193,fft:[1,3,7,12,14,15,88,111,112,143,281,355,356,478],fft_inc:[12,356],fft_lib:12,fft_path:12,fftbench:[355,488],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:449,fictiti:[6,200,201,226,229,233,282,298,387,407,411,449],field1:[470,474],field2:470,field:[],fifth:[311,426],figur:[1,3,8,11,12,289,466,467],fij:390,file0:280,file1:[11,13,280,325,339,364,474,476,480],file2:[11,13,325,339,364,474,476,480],file:[],file_from:192,filen:364,filenam:[3,12,13,38,41,56,188,191,193,194,195,203,206,207,208,209,210,211,212,214,219,280,284,287,290,291,292,295,296,299,300,325,326,352,353,354,364,365,371,372,377,387,393,394,396,404,419,420,421,426,430,431,432,433,440,441,451,452,453,454,455,458,465,466,467,470,471,476,480,487,495,497,498,499],filennam:476,filep:[3,191,194,471,476,499],filepo:296,fill:[7,9,168,193,285,326,358,366,377,422,433,472],filter:[194,203],final_integr:8,final_integrate_respa:8,finchham:[6,150,389],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,119,171,188,195,204,217,218,228,231,254,280,286,294,298,361,363,365,366,387,402,407,411,419,440,450,452,490,495],find_custom:8,fine:[16,17,172,200,226,324,366,370,495],finer:[142,168,495],finest:355,finger:[168,190,252,472],finish:[6,11,41,214,339,352,354,355,367,369,370,457,474,495,496],finit:[],finni:[7,393,450],finvers:224,fiorin:[9,219],fire:[2,361,362,363,365,483],firebrick:194,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,104,105,106,108,114,118,119,129,132,135,136,140,143,153,156,162,164,166,167,169,170,171,175,188,191,192,193,194,195,197,198,206,207,209,210,211,212,214,217,220,231,232,237,242,252,253,254,255,280,282,287,288,289,291,296,299,302,303,311,312,314,315,316,323,324,325,326,328,332,337,339,340,347,358,363,364,365,366,369,370,371,372,375,377,378,380,382,384,386,387,393,395,396,399,400,402,403,404,406,407,411,416,417,419,421,422,424,426,430,432,433,440,441,449,451,452,453,454,455,458,462,464,465,466,467,469,470,471,474,476,478,481,482,483,486,487,490,495,496,497,499],fischer:[6,9,19,20,174,382,481],fit:[3,6,9,12,38,56,188,298,314,372,377,404,419,424,445,452,454,477,495],five:[73,154,289,364,377,420,469,483],fix:[],fix_adapt:[162,199,415],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,204,285],fix_evapor:204,fix_flux:203,fix_gcmc:[204,364],fix_gl:233,fix_gld:233,fix_grav:285,fix_id:[3,218,253,255,257,258,259,260,261,262,263,286,289],fix_modifi:[],fix_mov:[190,332],fix_nh:8,fix_npt:233,fix_nvt:[204,231],fix_poem:[3,6],fix_pour:[3,221],fix_qbmsst:9,fix_qeq:[3,386],fix_rattl:302,fix_reax_bond:432,fix_rigid:[245,375],fix_saed_vtk:300,fix_setforc:8,fix_shak:302,fix_srd:3,fix_styl:260,fix_temp_rescal:320,fixedpoint:[218,255],fixextern:229,fixid:203,fji:390,flag1:[223,368],flag2:[223,368],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,94,104,105,107,120,163,167,171,191,193,194,195,212,217,219,223,236,239,243,245,251,252,281,288,299,311,313,314,321,325,334,337,353,356,364,368,369,370,372,401,406,419,422,449,464,466,467,469,470,471,473,474,475,479,495],flag_buck:381,flag_coul:[381,390,411],flag_lj:[390,411],flagfld:[379,416,417],flaghi:[3,379,416,417],flaglog:[379,416,417],flagn:223,flagvf:[379,416,417],flat:[6,326,331,332,336],flavor:[2,7,12],fld:[9,331,379,416,417],flen:373,flex_press:373,flexibl:[3,6,8,169,193,206,210,219,233,256,322,329,395,454,487],flip:[3,6,220,255,333,334],floor:495,flop:12,floralwhit:194,flow:[],fluctuat:[6,64,87,218,231,232,239,242,255,260,280,281,324,326,349],fluid:[],fluid_veloc:246,flush:[3,194,486],flux:[],flv:193,fly:[7,9,12,41,193,197,203,208,221,224,299,302,327,377,422,487,490],fmackai:9,fmag:222,fmass:282,fmax:[363,487],fmomentum:224,fmsec:[2,194,239,240,252,255,286,299,317,318,478,489,494,496],fname:354,fno:[12,16],fnorm:[363,487],fnpt:224,fnvt:224,foce:402,fock:373,focu:302,fogarti:[9,292,433],foil:[142,280,441],fold:[312,478],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,92,97,98,108,115,118,119,121,142,143,146,147,148,154,156,161,164,166,168,169,174,177,178,179,180,182,183,185,186,188,191,192,193,194,197,203,204,205,206,207,208,209,210,211,212,214,219,220,221,224,225,229,231,232,233,236,238,239,240,242,245,253,255,260,261,262,263,274,275,276,278,281,282,284,287,288,289,290,292,294,296,298,299,300,302,316,317,318,319,322,323,324,325,326,328,329,337,338,342,343,344,345,346,349,351,353,358,360,363,364,365,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,429,430,431,432,433,434,435,437,439,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,456,457,458,460,461,462,464,466,467,469,470,472,474,476,477,478,481,483,484,485,490,495,496,498],foo:[4,8,11,12,191,193,229,467,480,495],foot:6,footprint:[12,370],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:245,forcefield:[298,401],forcegroup:242,forcezero:361,ford:390,forestgreen:194,forev:71,forget:[240,490],forgiv:255,fork:[12,191],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,87,89,90,92,94,104,105,107,118,142,143,162,163,172,176,194,197,198,199,216,232,233,239,241,245,252,276,281,292,294,298,299,326,331,335,340,341,344,349,360,362,364,365,372,373,377,384,393,395,397,401,402,406,418,419,421,422,426,427,430,432,433,434,440,441,442,450,452,453,454,455,461,463,466,467,469,474,479,486,490,495],formal:[6,78,80,91,232,233,239,255,282,314,322,440],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,176,188,191,192,193,194,195,206,209,210,211,212,214,216,281,284,288,290,292,295,299,300,310,325,326,337,338,341,360,364,365,371,372,377,384,393,396,406,419,421,431,432,433,435,441,452,458,459,466,467,469,470,471,474,485,486,487,495,497],former:[6,12,16,39,41,194,214,326,330,377,379,475,481,495],formerli:[7,13],formul:[1,40,64,143,200,226,239,255,276,290,292,298,302,325,355,372,377,393,395,398,419,429],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,95,97,98,107,114,120,143,145,146,147,148,149,150,151,152,154,155,156,157,158,159,160,161,167,168,173,175,176,187,190,191,198,199,200,201,206,207,208,209,212,213,220,226,234,235,237,239,240,252,280,281,287,296,301,308,312,314,317,318,319,328,331,334,336,337,339,340,341,343,350,358,364,372,373,375,377,382,383,384,385,390,391,393,394,398,399,400,401,403,406,407,409,410,411,413,414,416,417,419,423,424,425,434,435,442,450,451,453,454,455,458,460,461,465,469,472,479,486,487,494,495,496],forth:[1,6,11,12,13,14,15,369,467,472,476],fortran:[3,6,9,11,12,13,229,393,402,419,432,433],fortun:8,forward:[3,8,87,354,365,370],foster:[377,429,430],foul:171,found:[3,6,9,12,73,162,191,217,219,231,236,242,281,321,327,339,354,366,384,387,390,464,470,471,486],four:[6,11,54,81,104,105,142,164,253,326,349,364,365,422,464],fourier:[],fourth:[6,106,298,311,321,382,426,440],fox:[6,120,174,448,481],fphi:[38,56,452],fpic:12,fplo:[38,56,452],fprime:452,fqdn:238,fqq:390,frac:[],fraction:[1,3,6,8,12,16,39,41,80,111,143,171,190,193,194,204,215,216,217,218,253,285,289,296,297,314,319,320,358,365,370,377,379,399,416,417,474,479],fragment:[42,236,296],fraig:[42,376],frame:[83,142,194,203,253,289,333,398],framer:[193,194],framework:[5,233,371,441],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,87,162,199,280,314,323,324,325,326,362,365,373,395,415,422,430,461,466],freedom:[3,6,8,95,97,98,100,102,103,114,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,161,206,217,224,231,233,239,240,245,255,256,260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nnner:413,inordin:327,inorgan:[6,458],inp:[219,339,441,458],input1:[65,68,69,79,93,110,115,116,117,119,121,316],input2:[65,68,69,79,93,110,115,116,117,119,121,316],input:[],input_doubl:3,inquir:304,insensit:12,insert:[3,5,7,8,12,59,168,197,221,231,237,285,355,441,449,467,473,490],insid:[2,3,6,8,11,71,131,137,168,191,194,205,210,211,221,222,228,231,237,242,245,285,299,314,331,333,334,335,336,337,353,358,409,467,468,469,471,472,479,483,495],insight:[6,13],instabl:[242,390,439],instal:[],instanc:[6,11,198,219,233,333,397,402,424,430,467,490],instantan:[6,63,217,218,232,233,255,260,281,286,289,294,296,299,321,475,487],instanti:[6,11,12,203,402,466],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,61,63,70,71,90,104,119,146,150,172,188,191,199,206,209,210,211,212,214,218,219,231,239,242,245,246,281,287,297,299,316,334,353,355,356,359,366,370,380,381,393,406,408,415,419,422,464,472,476,483,485,490,495],institut:[9,236,284],instruct:[],insuffici:[3,6,12],insult:255,insur:[3,6,11,12,17,39,40,61,73,103,105,168,169,188,191,193,194,200,215,216,221,226,227,228,229,231,234,239,251,287,288,297,299,314,326,331,335,336,337,339,354,364,366,370,385,398,402,428,434,452,466,467,469,470,474,477,478,486,487,495,496],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,108,115,117,119,121,142,166,168,171,172,174,178,179,183,188,190,191,193,194,204,206,210,211,215,216,217,221,223,229,231,232,233,236,239,240,241,242,281,284,285,288,289,294,299,314,316,318,321,325,326,345,355,358,379,391,392,405,419,432,433,437,439,441,464,466,467,468,469,477,478,479,483,486,495,496],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,208,232,431,469],intens:[1,3,6,9,63,66,74,75,86,89,90,91,94,104,105,106,107,114,116,118,119,120,121,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,163,164,165,167,197,206,207,209,210,211,212,214,215,216,217,225,228,235,245,253,255,260,296,299,300,314,322,326,328,329,486,487],intepol:495,inter:[14,18,42,61,62,148,171,172,191,217,239,241,254,291,299,355,365,377,479,490,495,497,499],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,42,44,50,54,55,57,61,63,65,69,72,77,79,87,88,92,93,108,109,110,112,114,117,118,124,125,126,127,129,130,131,132,133,134,135,137,138,139,140,142,143,144,146,147,161,162,166,169,170,171,172,173,174,176,180,181,187,191,197,198,199,215,216,217,230,231,236,237,239,241,245,269,280,282,284,290,292,298,299,305,306,314,315,321,326,330,331,332,335,336,341,342,343,344,346,350,355,356,363,364,365,366,367,368,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,429,430,433,434,435,437,439,440,441,442,449,450,451,453,454,455,456,457,458,459,460,461,462,464,467,469,471,473,474,478,479,481,486,487,490,497],interatom:[3,4,7,168,191,254,323,324,371,377,393,395,403,419,422,440,454,495],intercept:120,interchang:6,interconnect:18,interconvert:395,intereract:39,interesect:335,interest:[1,5,7,8,9,11,13,71,167,282,321,324,356,394,417,432,433,467,495],interf:370,interfac:[],interfer:[12,255,372],interg:[6,490],intergr:[478,482],interi:417,interior:[3,6,41,335,472],interlac:419,interleav:[6,168,477],intermedi:[6,12,59,193,254,280,349,365,467,468,477,481],intermix:464,intermolecular:372,intern:[0,2,3,5,6,9,11,16,20,21,24,28,32,35,36,39,40,42,63,87,100,102,120,143,148,150,167,175,188,193,194,197,198,199,203,216,220,224,236,248,249,253,255,260,281,299,303,340,342,346,349,353,363,364,443,444,452,467,469,471,474,483,486,487,494,495,496,497],internal_element_set:203,internal_quadratur:203,internet:238,interpenetr:419,interpentr:[444,445,447],interpol:[6,15,38,56,101,188,193,194,203,242,280,355,356,365,377,424,433,446,452,453],interpret:[2,6,11,193,209,399,442,464,467,483,495],interrupt:289,intersect:[3,6,120,194,335,337,472],intersert:335,interspers:363,interstiti:[166,422],intertia:[3,94],interv:[3,6,91,192,207,239,255,289,294,295,306,440,446,464,483,495],intestieti:120,intial:[6,370,372],intiial:[41,474],intiti:[3,313],intra:299,intra_energi:231,intramolecular:[29,231],introduc:[6,9,92,108,193,255,289,294,299,349,355,371,387,395,407,411,415,451,483,495],introduct:[],intsal:[],intuit:358,inv:[120,167,300],invalid:[3,12,71,89,171,269,365,416,417,471],invari:[108,135,140,142],invent:302,invers:[],invert:[1,6,172,281],invis:335,invoc:[166,217,370,437,439,467],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,87,88,89,90,94,104,105,107,111,112,113,114,119,145,155,162,163,166,168,169,171,172,174,175,177,178,179,180,182,183,185,186,188,191,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,225,226,227,228,229,230,231,232,234,235,236,237,239,240,241,242,243,244,245,246,247,248,249,251,252,254,255,257,258,259,260,261,262,263,264,265,266,267,268,269,270,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282],redefin:[3,471,477,495],redirect:12,redo:12,reduc:[],reduct:[18,19,119,120,167,253,289,355],redund:396,ree:445,reed:[253,289],rees:[7,9,13],ref:[323,324,362],refactor:6,refer:[],referenc:[3,6,12,63,68,71,116,191,197,207,212,231,288,328,356,387,401,426,434,467,487,495],reflect:[],reformat:7,refresh:203,reg:472,regard:[6,59,252,302,307,429,433],regardless:[15,71,168,171,190,209,210,220,239,255,257,258,259,261,262,263,286,299,308,314,370,466,472,479],regim:[6,322,329,388,478],region:[],region_spher:8,region_styl:335,regist:[8,118,144,310,432,433],regoin:6,regress:495,regspher:168,regstrip:337,regul:6,regular:[1,3,9,41,62,88,166,170,191,204,214,231,326,356,388,466,469,471,473],reigon:495,reinhardt:[323,324],reject:[168,217,432,484],rel:[1,6,14,27,36,41,59,71,92,104,124,132,142,146,150,151,153,168,177,194,197,204,210,214,220,221,224,231,237,240,251,252,276,280,285,294,296,297,303,311,314,316,321,322,326,333,337,355,356,363,395,398,399,416,417,419,434,461,470,478,483,487,490,496],relat:[],relatic:[],relationship:[6,290,339,355,440,461,490,495],relax:[],releas:[0,5,7,8,13,215],relect:[3,424],reles:42,relev:[2,6,12,41,78,80,113,130,168,172,194,198,199,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,220,221,222,225,227,228,230,231,232,235,236,242,243,244,246,247,248,249,251,252,254,264,265,266,267,268,269,270,271,272,273,279,283,284,285,287,288,291,293,295,296,297,300,301,302,303,308,312,314,315,316,321,322,325,326,327,328,329,330,331,332,333,334,336,337,355,363,373,374,379,385,387,388,390,391,392,395,397,398,399,400,401,406,408,409,410,412,413,414,416,417,424,425,429,434,442,449,452,460,461,462,466,482,496],reli:[3,12,291,395,433,462,469,479],reloc:12,remain:[7,12,33,37,41,50,55,59,71,87,105,148,149,150,151,155,156,157,158,160,171,181,187,188,191,198,199,204,206,207,210,211,218,220,239,240,247,255,256,261,262,263,274,275,276,278,283,284,306,314,317,318,319,325,326,337,339,347,350,364,377,395,402,415,422,424,450,464,469,470,474,479,481,483,487,490,495,496],remaina:377,remaind:[168,191,221,285,314,327,455,469],remap:[3,6,12,59,61,71,151,168,190,210,220,237,252,276,355,469,470,471],remedi:[6,490],rememb:2,remov:[2,3,6,8,9,13,54,71,72,77,92,108,116,118,142,146,147,148,149,150,151,155,156,157,158,160,161,168,171,172,197,206,210,215,228,239,240,245,251,253,255,261,262,263,274,275,276,278,284,290,299,300,302,314,317,318,319,321,337,355,365,390,417,422,469,472,480,481,495,496],remove_bia:8,remove_bias_al:8,remove_molecul:203,remove_sourc:203,remove_speci:203,ren:167,renam:[12,338,480],render:[12,13,191,193,194],rendon:[255,256],reneighbor:[3,8,12,39,57,71,210,214,231,314,327,337,391,486,487],renssela:284,renumb:71,reorder:[3,12,39,466],repeat:[2,6,193,194,210,217,218,231,307,358,377,453,455,457,464,483],repeatedli:2,repel:237,repes:191,replac:[2,3,6,11,12,41,63,89,90,119,145,146,147,148,149,150,151,154,155,156,157,158,160,161,191,193,194,195,206,207,209,210,211,212,214,217,221,239,260,287,294,296,387,409,470,471,476,477,487,495,496,497,499],replic:[],replica:[],replica_fil:12,report:[],repositori:[7,12,403,431,432,433],reprens:326,repres:[1,3,6,8,9,12,15,40,41,42,59,67,71,90,115,118,180,188,191,193,206,207,208,209,210,211,212,218,224,232,234,239,242,255,282,284,286,294,299,300,303,311,326,328,335,356,365,371,377,398,405,415,416,417,419,420,421,427,430,432,433,456,457,464,466,469,479,481,484,490,495,497],represent:[3,6,8,9,57,59,136,170,191,232,233,282,326,377,395,398,422,434,469,472,490],reprocess:474,reproduc:[3,255,332,387,393,399],repul:419,repuls:[6,7,9,36,40,45,46,110,237,290,331,332,335,372,376,377,385,387,391,395,399,401,415,419,423,440,449,455,458,461,462,479],reqir:[290,292],request:[3,6,8,12,41,104,171,188,191,236,242,297,314,316,353,355,424,432,433,464,474,479,483,495,496,497],requir:[],rerun:[],rescal:[],research:[5,7,242,246,422,464,483],resembl:294,reserv:[12,236,490],reservoir:[91,231,235,239,326],reset:[],reset_atomic_reference_posit:203,reset_dt:8,reset_target:8,reset_tim:203,reset_timestep:[],resid:13,residu:236,residue1:366,resist:[6,236],resolut:[208,440,452],resolv:[218,282,314,417],resort:3,resourc:[7,371,393],respa:[3,16,225,236,255,368,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,390,391,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,423,425,427,429,431,432,433,434,435,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,457,458,460,461,462,477,478,489,495],respecifi:422,respect:[1,6,9,10,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,45,46,47,48,49,51,53,54,56,59,70,71,87,89,97,98,111,114,120,124,145,150,153,155,162,166,167,174,175,177,178,179,180,182,183,185,186,188,193,194,210,211,216,217,218,220,234,237,239,240,242,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,290,291,299,300,303,311,313,326,331,334,340,342,343,345,346,349,351,353,355,356,360,363,364,369,370,371,372,374,376,377,378,379,380,381,382,383,385,386,387,390,391,393,394,396,397,398,399,400,401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86,299,452,490],suspect:3,suspens:[416,417],sustain:[191,218,399],suzuki:[255,299],svg:6,svn:[7,11,12],sw_exampl:431,swamp:299,swap:[],swegat:325,swiggl:[3,252,331,334,336,472,495],swiler:[142,441],switch7_section_start:397,switchflag:[142,441],swm4:490,swol:53,swope:6,sxx:194,sy0302:9,symbol:[6,12,120,167,296,377,395,441],symmetr:[6,70,87,94,114,133,134,135,138,139,140,143,198,199,218,255,256,322,329,371,384,390,393,453,455,495],symmetri:[3,5,6,7,8,63,64,70,92,108,170,191,253,280,340,356,371,469,490],sync:[3,6,488],synchron:[1,233,365,488],synechococcu:7,syntax:[],sysdim:281,sysmt:17,sysstem:377,syst:440,system:[],system_:282,systemat:[6,9,208,231,239,422],systemx:3,t10:484,t11:484,t12:484,t13:484,t14:484,t15:484,t3e:12,t_chain:3,t_corr:3,t_correl:464,t_dephas:464,t_e:326,t_e_min:326,t_equil:[323,324],t_event:[3,464,483],t_hi:483,t_infil:326,t_init:[289,326],t_iter:3,t_j:29,t_lb:242,t_lo:483,t_order:3,t_oufil:326,t_out:326,t_outfil:326,t_qm:289,t_switch:[323,324],t_target:379,ta06a:441,ta4:422,ta5:167,ta6:422,tab:[2,469],tabbernor:120,tabinn:424,tabul:[3,7,13,22,37,38,44,55,56,65,71,79,93,188,314,355,371,377,378,380,381,382,383,384,387,393,395,407,411,418,427,430,433,435,450,452,453,459,471],tabular:430,tabulate_long_rang:433,tad:[],tadmor:9,tag:[203,490],tagint:3,tail:[3,87,112,162,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,390,391,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,457,458,460,461,462,487,495],tailor:[71,327],tait:[9,447,448],taitwat:[],take:[1,2,3,6,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,56,59,77,87,89,91,111,114,115,118,119,143,145,155,162,166,172,174,175,176,177,178,179,180,182,183,185,186,188,191,193,194,198,199,200,213,214,218,220,227,230,234,238,239,240,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,291,299,301,302,311,312,313,314,316,317,318,319,327,330,334,337,340,341,342,343,345,346,349,351,355,356,360,370,371,372,374,377,378,379,380,381,382,383,384,385,386,387,390,391,393,394,396,397,398,399,400,401,405,407,408,409,410,411,412,413,414,415,416,420,422,425,426,427,429,432,433,434,435,440,442,449,451,452,453,454,455,456,457,458,460,461,462,463,467,470,472,477,478,479,486,487,488,495],taken:[6,59,150,168,190,217,221,231,232,233,239,240,241,242,285,289,292,326,345,393,395,398,451,458,464,478,479],talk:[6,7],talli:[],tan:[194,495],tandem:[4,16,299],tang:422,tangent:[42,254],tangenti:[6,110,314,332,336,376,399],tanh:326,tantalum:[4,422,441],taper:[3,292,418],tar:12,tarbal:[0,8,11,12],target:[3,6,7,8,9,11,12,17,39,41,194,202,214,218,219,221,231,232,233,239,240,241,255,256,257,258,259,260,261,262,263,274,275,276,277,278,282,286,289,294,299,303,312,317,318,319,320,325,326,329,330,333,353,356,379,391,464,475,477,496],target_fil:325,task:[1,6,7,12,13,14,15,16,17,18,54,194,236,282,327,370,467,488],taskset:16,tatb:[4,295],tatom:490,tau:[3,157,208,239,240,242,255,286,299,317,318,323,324,326,489,494],tau_1:232,tau_k:232,tau_n_k:232,tb3:167,tbead:160,tbp:377,tchain:[255,256,260,276,277,299],tcl:294,tcom:240,tcsh:[11,12,384],tdamp:[239,255,256,260,299,317,318],tdephas:464,tdrude:[153,224,240,490],teal:194,tech:[7,9,13],technic:[6,7,9,242,292,314,433],techniqu:[6,7,9,87,197,218,253,289,299,330,333,356,424,452,490],technolgi:9,technolog:[9,14,19,236],tell:[2,6,11,12,37,55,187,197,281,350,366,432,433,450,467,471,490],telsa:17,temeperatur:11,temp:[],temp_drud:490,temp_eff:98,tempcom:[146,147,161],temper:[],temperar:282,temperatur:[],temperature_definit:203,tempfix:484,templ:[7,9,18],templat:[3,8,13,17,19,40,168,169,171,221,231,285,299,302,364,469],templeton2010:203,templeton2011:203,templeton:[9,203],tempor:232,temporari:[2,476],temporarili:[188,298,482,483],ten:14,tend:[29,255,280],tensil:[7,220],tensor:[3,6,8,63,82,83,89,90,91,94,107,114,129,132,133,134,135,138,139,140,142,143,144,145,146,147,148,149,150,151,152,154,155,156,157,158,159,160,161,218,242,245,255,256,260,284,286,299,329,355,356,364,395,416,417,422,437,439,487,495],tenth:[129,354],term:[0,1,3,5,6,7,8,9,12,20,21,22,27,38,40,45,46,61,87,88,89,91,112,114,143,144,146,147,156,161,162,175,176,177,188,194,198,199,205,207,209,212,220,226,232,233,234,239,240,241,242,254,255,256,257,258,259,260,261,262,263,274,275,276,278,282,286,289,298,299,312,317,318,319,326,328,330,332,340,341,351,355,363,366,371,372,377,378,379,380,381,382,383,385,386,387,388,389,390,391,393,394,395,396,398,399,400,407,411,414,415,416,417,419,420,421,422,424,427,434,440,449,451,453,454,455,458,461,478,479,481,487,490],termin:[120,255,363,365,437,439,468,477],termostat:318,terrel:362,terri:7,tersoff:[],tersoff_1:[453,454,455],tersoff_2:[453,454,455],tersoff_mod:454,tertiari:180,tessel:[9,166],test:[],test_descriptor_str:3,testf:188,testu:188,tether:[6,297,303,311,313,324,397],tetot:[9,440],tex:8,texa:429,texas_holdem:298,text:[2,3,4,6,7,8,12,13,38,41,56,188,191,193,194,197,203,206,207,208,209,210,211,212,214,219,236,287,325,326,338,356,358,365,393,396,406,419,441,452,465,469,470,486,495,497],textur:17,tfac_insert:231,tfactor:[3,194],tfinal:495,tfix:298,tfmc:[],th4:167,than:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,27,38,39,40,41,42,56,57,58,59,61,63,68,71,76,86,88,92,106,108,110,114,117,118,121,143,166,169,170,171,177,188,190,191,192,194,197,202,204,206,209,210,211,212,214,215,216,217,218,220,221,222,225,228,231,232,233,234,237,238,239,242,253,280,281,285,286,287,288,289,290,292,294,297,298,299,300,303,304,310,311,312,314,318,319,321,322,326,329,330,331,332,333,334,335,336,337,339,355,356,361,362,363,364,365,366,367,370,375,376,377,378,380,381,382,393,395,398,399,405,416,417,419,424,432,433,434,440,442,449,450,451,452,455,457,459,461,462,464,465,466,467,469,470,471,472,473,474,477,478,481,483,484,486,495,496,497],thank:[236,453,455],thb:433,thb_cutoff:433,thb_cutoff_sq:433,thei:[0,1,2,3,4,6,7,8,11,12,13,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,37,38,39,40,41,42,43,45,46,47,48,49,51,53,54,55,56,57,59,61,63,64,66,68,70,71,74,75,81,82,84,87,89,90,91,94,104,105,107,110,111,114,116,117,118,119,121,142,145,146,148,150,151,154,155,161,163,165,168,170,171,172,174,175,177,178,179,180,182,183,185,186,187,188,191,193,194,197,198,199,200,202,205,206,207,209,210,211,212,213,214,215,216,217,218,220,221,226,227,230,231,232,234,235,236,239,240,242,245,252,255,257,258,259,260,261,262,263,264,265,266,267,272,274,275,276,278,284,285,286,287,288,290,291,298,299,300,301,302,314,315,317,318,319,321,325,326,328,329,330,332,334,335,337,339,340,342,343,344,345,346,349,350,351,353,355,356,358,360,362,363,364,365,366,369,370,371,372,374,375,376,377,378,379,380,381,382,383,384,385,386,387,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,405,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,425,426,427,429,430,432,433,434,435,440,441,442,449,450,451,452,453,454,455,456,457,458,459,460,461,462,465,467,469,470,471,472,473,474,478,479,481,482,487,490,495,497,498],them:[1,2,3,4,6,7,8,9,11,12,13,14,17,39,40,41,54,59,71,91,104,109,116,119,121,144,170,175,191,193,194,195,205,206,207,209,210,211,212,214,217,218,220,228,236,239,240,251,255,257,258,259,260,261,262,263,274,275,278,280,286,288,296,297,298,299,302,314,317,318,319,321,325,326,328,332,333,334,336,337,340,356,358,364,365,366,370,371,377,384,393,396,398,402,424,434,442,457,464,467,469,476,481,484,490,495,496],themselv:[6,11,171,198,199,214,240,355,356,365,367,371,377,387,393,415,419,420,421,441,495],theor:321,theorem:[232,239,377],theoret:[106,236,289,451],theori:[3,6,9,12,40,142,203,219,233,255,281,355,356,377,422,461,483],thereaft:[71,247,283,299,322,329,467],therebi:[327,416,417],therefor:[3,6,12,64,87,153,224,231,240,242,302,321,356,389,431,433,451,456,478,490],therein:[6,419],thereof:87,thermal:[],thermo:[],thermo_modifi:[],thermo_p:[3,63,111,467,487],thermo_press:[63,114,218,224,255,257,258,259,260,261,262,263,286,486,487,490],thermo_styl:[],thermo_temp:[63,114,145,217,218,231,255,257,258,259,260,261,262,263,274,275,276,278,281,286,317,318,319,486,487,490],thermoberendsen:6,thermochem:494,thermochemistri:395,thermodyam:[487,494],thermodyanm:[63,217,314,337,478],thermodynam:[],thermophys:424,thermost:[6,150,202,219,224,240,333,490],thermostat:[],thermostatequ:6,thesi:[355,356,416,431],thess:378,theta0:[20,21,24,26,27,28,32,33,35,36,142,177,298,349],theta0max:142,theta10:377,theta1:[175,340,377],theta2:[175,340,377],theta3:[340,377],theta4:377,theta5:377,theta6:377,theta7:377,theta8:377,theta9:377,theta:[3,6,26,27,37,38,63,65,80,92,108,142,167,168,177,190,193,234,294,298,326,340,349,401,430,454,469,472,479],theta_0:426,theta_:[349,377],theta_c:401,theta_ijk:377,theta_ijl:340,theta_jik:[420,421],theta_pi:377,theta_sigma:377,thex:290,thi:[0,1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style body/rounded/polygon command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":215,"default":[37,39,40,55,57,58,59,61,62,71,87,88,92,103,104,106,108,109,120,124,125,142,148,156,157,161,167,168,171,173,187,189,190,191,193,194,195,196,198,199,200,202,203,204,206,210,211,212,215,216,218,219,220,221,225,228,231,232,237,239,240,241,242,243,245,250,253,255,256,260,276,277,281,282,285,286,287,288,289,291,294,296,297,299,300,314,316,321,322,323,324,327,329,331,333,337,350,353,355,356,358,359,361,362,364,366,367,368,370,373,377,379,395,416,417,422,424,432,433,449,450,464,465,466,469,470,472,474,476,477,478,481,483,485,486,487,488,489,494,496,497,498],"function":495,"long":[208,378,380,381,382,383,387,389,390,407,411,415,427,435],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[198,199],addforc:200,addit:[12,13],addtorqu:201,adiabat:6,adjust_dt:304,adp:371,airebo:372,alloi:393,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:202,arrai:6,aspher:[6,82,146,257,261,265,266,274],atc:[9,203],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,92,96,97,100,101,102,108,112,113,115,142,143,166,202,204,205,288,495],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:213,awpmd:[9,373],balanc:[41,214],barostat:6,basal:67,beck:374,berendsen:[286,317],between:6,binary2txt:13,bodi:[6,8,42,68,147,258,262,267,275,375,376],bond:[8,13,69,215,216,217,295],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:377,born:[378,389],boundari:[7,57],box:[6,58,218],brownian:379,buck:[380,381,389,418],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,174,382,415],chunk:[6,66,71,75,90,94,105,107,116,148,163,165,206],citat:7,class2:[21,43,175,340,383],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[331,385,461],colvar:[9,13,219],com:[74,75,149],comb3:386,comb:[291,386],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,495],compute_modifi:103,condit:7,conduct:[6,322],constant:6,constraint:7,contact:76,contact_radiu:122,coord:77,core:6,correl:[207,208],cosin:[23,24,25,26,27,28,177],cossq:342,coul:[378,380,381,382,383,387,388,389,400,407,411,415,427,435],coupl:6,creat:216,create_atom:168,create_bond:169,create_box:170,createatom:13,creation:7,csld:318,csvr:318,cubic:409,cuda:[9,14,111,114,145,155,200,213,227,230,234,255,264,301,302,317,319,330,378,380,382,383,393,399,400,407,408,410,413,425,451,453],custom:8,cut:[49,373,380,383,387,390,395,397,407,408,415,423,427],cvff:343,damag:[78,123],data2xmovi:13,data:6,databas:13,deby:[387,407],dec:0,deform:[151,152,220],delete_atom:171,delete_bond:172,delta:24,deposit:221,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],diagnost:7,diel:388,dielectr:173,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:176,dihedral_styl:[2,174,175,177,178,179,180,181,182,183,184,185,186,187,188],dilat:80,dimens:189,dipol:[6,29,390],direct:224,discuss:6,disp:6,displac:[81,86],displace_atom:190,distanc:344,distribut:[7,12],document:0,dpd:391,drag:222,dreid:[6,401],drude:[6,9,153,223,224,240],dsf:[387,407],dsmc:392,dump:[6,8,191,192,193,195],dump_modifi:194,dynam:290,eam:[13,393],echo:196,edip:394,eff:[9,13,97,98,152,154,159,241,256,268,277,320,395],efield:226,eim:396,elast:6,emac:13,enforce2d:227,ensembl:7,erot:[82,83,84,85],error:3,evapor:228,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],exp:[27,177],expand:[46,410],extend:[8,11],extern:229,fcc:280,featur:[7,8,495],fene:[45,46],fep:[9,13,87,199],field:[6,7],file:6,finit:6,fire:290,fix:[2,6,8,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,495],fix_modifi:[198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,2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09,110],pair_coeff:384,pair_modifi:424,pair_styl:[2,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,460,461,462],pair_writ:459,pairwis:8,parallel:11,paramet:6,pars:2,partial:155,particl:[6,7,42],partit:463,past:5,per:6,perform:[1,10],peri:429,period:25,phonon:[9,13,281],pimd:282,piston:333,planeforc:283,plastic:113,plastic_strain:126,plastic_strain_r:127,pmb:429,poem:[9,284],point:290,polariz:6,poli:[379,416,417],polygon:376,polym:13,polymorph:430,post:7,potenti:[2,6,8],pour:285,pppm:6,prd:464,pre:7,press:286,pressur:114,previou:12,print:[287,465],problem:[3,4],process:[6,7],processor:466,profil:156,properti:[6,115,116,117,288],pymol_aspher:13,python:[9,11,13,467],qbmsst:289,qeq:[290,291,292],qmmm:[9,293],qtb:[9,294],quadrat:186,quantiti:6,quartic:[35,54],quip:431,quit:468,ramp:157,rattl:302,rdf:118,read_data:469,read_dump:470,read_restart:471,reax:[9,13,292,295,296,432,433],reaxc:9,rebo:372,recent:297,reduc:119,refer:495,reflect:334,region:[8,119,158,159,335,472,495],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,97,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,185,186,187,188,189,190,191,192,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,228,230,231,232,233,234,235,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,294,295,296,297,299,300,301,303,304,305,306,307,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,349,350,351,352,353,354,355,356,358,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,474,475,476,477,478,479,481,482,483,484,485,486,487,488,489,491,492,493,495,496,497,498,499],relax:218,replic:473,replica:[6,7],report:3,requir:12,rerun:474,rescal:[319,320],reset:225,reset_timestep:475,resquar:434,restart2data:13,restart:[6,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,476],restrain:298,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],rho:128,rhosum:446,rigid:[6,83,99,245,299],ring:349,rotat:160,round:376,rule:2,run:[6,11,12,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,477],run_styl:478,scalabl:10,scalar:6,screen:12,script:[2,6,8,11],sdk:[36,435],self:313,serial:11,set:[6,479],setforc:301,setvel:308,shake:302,share:[11,12],shell:[6,480],shield:290,shift:[26,27,48,49,177],simpl:31,simul:6,size:6,slater:290,slice:121,sllod:[276,277],small:299,smd:[9,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,303,304,305,306,307,308,310,436,437,438,439],smooth:[413,414],smtbq:[9,440],sna:142,snad:142,snap:441,snapshot:6,snav:142,soft:[415,442],solver:2,sourc:7,spatial:[210,211],spc:6,speci:296,special:[7,424,495],special_bond:481,sph:[9,443,444,445,446,447,448],sphere:[84,85,161,211,245,259,263,272,278],spheric:6,spline:[420,421],spring:[311,312,313,324],squar:28,srd:[314,336],srp:449,standard:9,start:[12,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336],state:316,stationari:249,stop:[198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336],store:[315,316],strategi:1,streitz:387,stress:[143,144],structur:2,style:[1,2,6,8],submit:8,suffix:482,summari:6,swap:[204,217],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,281,282,283,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],system:6,tabl:[0,6,38,56,188,452,453],tad:483,taitwat:[447,448],talli:144,temp:[145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,317,318,319,320],temper:484,temperatur:6,tersoff:[453,454,455],test:11,tfmc:321,thermal:[6,322],thermo:[6,485],thermo_modifi:486,thermo_styl:487,thermodynam:[6,8],thermostat:6,thole:456,time:[6,212],timer:488,timestep:489,tip3p:6,tip4p:[6,387,407,411,415],tip:12,tlsph:437,tlsph_defgrad:129,tlsph_dt:130,tlsph_num_neigh:131,tlsph_shape:132,tlsph_strain:133,tlsph_strain_rat:134,tlsph_stress:135,tmd:325,tool:[12,13],torqu:163,transform:224,tri:[273,457],tri_surfac:438,triangle_mesh_vertic:136,triclin:6,tstat:391,ttm:326,tune:327,type:7,ulsph:439,ulsph_num_neigh:137,ulsph_strain:138,ulsph_strain_r:139,ulsph_stress:140,umbrella:351,uncomput:491,undump:492,unfix:493,unit:494,user:[9,12,14,16,18],vacf:164,valu:[6,495],variabl:[6,8,495],variou:1,vashishta:458,vcm:165,vector:[6,328,495],veloc:496,version:[0,5,12],via:12,vim:13,viscos:[6,329],viscou:[246,330],visual:6,vol:141,voronoi:[9,166],vtk:300,wall:[6,331,332,333,334,335,336],wall_surfac:310,warn:3,water:6,weight:209,what:[7,12],wolf:[378,387],wrapper:11,write:6,write_data:497,write_dump:498,write_restart:499,xmgrace:13,xmovi:13,xrd:167,xtc:9,yukawa:[460,461],zbl:[455,462]}}) \ No newline at end of file
    property/atom qeq/comb (o) qeq/dynamicqeq/fire qeq/point qeq/shielded qeq/slater reax/bondsrecenter
    restrain
    recenterrestrain rigid (o) rigid/nph (o) rigid/npt (o) rigid/nve (o) rigid/nvt (o) rigid/small (o)rigid/small/nph
    rigid/small/npt
    rigid/small/nphrigid/small/npt rigid/small/nve rigid/small/nvt setforce (ck) shake (c) spring spring/rgspring/self
    srd
    spring/selfsrd store/force store/state temp/berendsen (c) temp/csld temp/csvr temp/rescale (c)tfmc
    thermal/conductivity
    tfmcthermal/conductivity tmd ttm tune/kspace vector viscosity viscous (c)wall/colloid
    wall/gran
    wall/colloidwall/gran wall/harmonic wall/lj1043 wall/lj126 wall/lj93 wall/piston wall/reflect (k)wall/region
    wall/srd 
    wall/regionwall/srd